G2C::Proteomics

Comparative analysis of human and mouse postsynaptic proteomes identifies high compositional conservation and abundance differences for key synaptic proteins

Àlex Bayés1,2,3*,Mark O Collins4*, Mike DR Croning2,3, Louie N van de Lagemaat2,3, Jyoti S Choudhary4 and Seth GN Grant2,3*

Corresponding authors: Seth.Grant@ed.ac.uk, ABayesP@santpau.cat

  1. Molecular Physiology of the Synapse Laboratory, Institut de Recerca de l’Hospital de la Santa Creu i Sant Pau, UAB. C/ Sant Antoni Maria Claret 167, 08025 Barcelona, Catalonia, Spain
  2. Genes to Cognition Programme, The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
  3. Centre for Clinical Brain Sciences and Centre for Neuroregeneration, The University of Edinburgh, Chancellors Building, 47 Little France Crescent, Edinburgh EH16 4SB, UK
  4. Proteomic Mass Spectrometry. The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK

 

Overview

Direct comparison of protein components from human and mouse excitatory synapses is important for determining the suitability of mice as models of human brain disease and to understand the evolution of the mammalian brain. The postsynaptic density (PSD) is a highly complex set of proteins organized into molecular networks that play a central role in behavior and disease. We report the first direct comparison of the proteome of triplicate isolates of mouse and human cortical PSDs. The mouse PSD (mPSD) comprised 1556 proteins and the human PSD (hPSD) 1461.

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A large compositional overlap was observed; more than 70% of hPSD proteins were also observed in the mPSD. Quantitative analysis of PSD components in both species indicates a broadly similar profile of abundance but also shows that there is higher abundance variation between species than within species.

Well-known PSD components are generally more abundant in the mouse PSD. Significant inter-species abundance differences exist in some families of key PSD proteins including glutamatergic neurotransmitter receptors and adaptor proteins. We have identified a closely interacting set of molecules enriched in the human PSD that could be involved in dendrite and spine structural plasticity. Understanding synapse proteome diversity within and between species will be important to further our understanding of brain complexity and disease.

The full results and analyses of the study can be sorted, searched and downloaded

Figures

Figure 1.
Validation of fractionation method and quantitative comparison of mouse and human cortical PSDs.
Figure 2.
Analysis of evolutionary conservation of PSD proteins in mouse and humans.
Figure 3.
Inter-species differences in postsynaptic density proteins.
Figure 4.
Bioinformatic functional analysis of proteins enriched in the human PSD.
Figure 5.
Predicted functional protein groups with the mammalian cortical PSD.

Figure 1. Validation of fractionation method and quantitative comparison of mouse and human cortical PSDs.

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a. Immunoblots of known postsynaptic density components. Mouse synaptosomes (S) and PSD (P) fractions are analysed for each of the three replicates. All proteins show enrichment in the PSD compared to synaptosomes. The presynaptic marker synaptophysin (Syn) is only detected in the synaptosomal fraction.

Only genes identified in triplicate in both species were considered for the quantitative analysis. Correlations are calculated based on linear models. Coefficients of correlations are represented by r.

b. Intra-species protein abundance correlation, human PSD first replica against second

c. Intra-species protein abundance correlation, mouse PSD first replica against second.

d. Plot of average values of PSD proteins abundance from human and mouse cortex.

e. Protein abundance correlation of PSD components found in the NMDA receptor complex [3];

f. Protein abundance correlation of PSD components found in the PSD-95 complex [26].

g.Protein abundance correlation of PSD components found in the mGluR5 complex [27].

h. Clustering of PSD protein abundance values for human and mouse replicates.

Figure 2. Analysis of evolutionary conservation of PSD proteins in mouse and humans.

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a.Median dN/dS of proteins identified in the human PSD, mouse PSD and mouse consensus set (cPSD) compared with the median genomic value.

b.Comparison of dN/dS values in proteins exclusive or enriched in one species with all PSD proteins.

Figure 3. Inter-species differences in postsynaptic density proteins.

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a.Venn diagrams showing the total amount of proteins in mPSD and hPSD as well as the overlap between them relative to the hPSD.

b.Venn diagrams showing the proteins identified in triplicate for the mPSD and hPSD, the overlap relative to hPSD between the two sets is also shown.

c.Immunoblot validation of proteins identified only in the hPSD by mass spectrometry. The following samples were analysed: H-M, mouse brain homogenate; H-H, human brain homogenate; and SX, each of the three synaptosomal fractions, PX, each of the three postsynaptic density fractions for both species.

d.The abundance fold difference (AFD) between mouse and human is shown for members of adaptors, channels and neurotransmitter receptors protein families. AFD is calculated as the mouse to human ratio of normalized and log2 transformed average abundance values. For each protein family the number of proteins displayed is given in brackets.

Figure 4. Bioinformatic functional analysis of proteins enriched in the human PSD.

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a.Ontology hierarchical tree leading to the Biological Process ‘Cellular Component Morphogenesis’. In red are the terms significantly enriched in proteins abundant in the human PSD.

b.Molecular interaction map of proteins from the human PSD that belong to the Biological Process ‘Cellular Component Morphogenesis’ (CCM) or are known to be involved in semaphorin signaling. Only CCM proteins enriched in the human PSD are considered. Some proteins related to semaphorin signaling are not enriched in either species, these are identified with a white name. Proteins highly interconnected are represented in clusters of different colors. Clustering was done using the Markov Clustering Algorithm (MCL) in BioLayout Express 3D [24]. Node edges are coloured according to a confidence score, from red (100% confidence) to blue (40% confidence).

Figure 5. Predicted functional protein groups with the mammalian cortical PSD.

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The mammalian cortical PSD was defined by combining all proteins identified in mouse and human. This set of PSD proteins were then functionally classified using the Panther Classification descriptor ‘Protein Class’. Enrichment analysis was done comparing the number of PSD proteins per class with the genome. The Panther Protein Class ontology is hierarchically organized, only end-branch classes are displayed to remove redundancy from the graph (all data in Table S8). Protein classes that did not show difference with the genome after correction for multiple testing, are shown in blue. Classes overrepresented are shown in red and classes underrepresented are shown in green.

Tables

Table 1.
Significantly enriched protein classes of species-specific PSD proteins.
Table 2.
Abundance of canonical PSD components as defined by studies with rodent brains.

Table 1. Significantly enriched protein classes of species-specific PSD proteins.

PANTHER Protein Class Proteins Identified p-value Proteins Identified p-value  
PANTHER Protein Class PSD Proteins Consensus PSD Proteins Enriched In
Cytoskeletal protein361.30E-09163.60E-07Human
Actin family cytoskeletal protein227.60E-08103.40E-05Human
Oxidoreductase395.20E-09135.10E-04Human
Dehydrogenase224.50E-0888.90E-04Human
Non-motor actin binding protein143.40E-0661.40E-03Human
Reductase81.10E-0341.40E-02Human
Transferase701.40E-08182.50E-02Human
Microtubule family cytoskeletal protein115.90E-0353.30E-02Human
Transfer/carrier protein148.50E-0364.30E-02Human
Membrane trafficking regulatory protein164.70E-0844.30E-02Human
Nucleotide kinase103.40E-0634.30E-02Human
Membrane traffic protein274.70E-0853.00E-01Human
Kinase401.20E-0783.00E-01Human
Protein kinase251.20E-0357.60E-01Human
Enzyme modulator336.50E-0377.90E-01Human
G-protein modulator158.50E-0311.00E+00Human
Ribosomal protein298.00E-13162.30E-09Mouse
Calcium channel72.90E-0463.90E-05Mouse
RNA binding protein601.20E-13203.90E-04Mouse
Ion channel313.70E-08122.10E-03Mouse
Nucleic acid binding786.70E-09282.50E-03Mouse
SNARE protein81.10E-0449.40E-03Mouse
Transporter574.10E-06198.80E-02Mouse
Ligand-gated ion channel119.60E-0442.20E-01Mouse
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Table 2. Abundance of canonical PSD components as defined by studies with rodent brains.

Mouse to human abundance difference of proteins known to be key components of the postsynaptic density, as derived from studies on mouse and rat brains. Abundance is expressed as the fold of mouse to human average abundance values.

Appr Gene (m) Appr Gene (h) Abundance Fold Difference (Mouse/Human) Significantly Enriched in Appr Gene (m) Appr Gene (h) Abundance Fold Difference (Mouse/Human) Significantly Enriched
Ablim1ABLIM11.3Gria3GRIA34.3Mouse
Baiap2BAIAP23.1Gria4GRIA423.8Mouse
BegainBEGAIN10.4MouseGrin1GRIN17.7Mouse
Cacng2CACNG22.6Grin2aGRIN2A5Mouse
Camk2aCAMK2A1Grin2bGRIN2B7.5
Camk2bCAMK2B3.4Homer1HOMER13.7Mouse
Camk2dCAMK2D0.9Homer2HOMER21.7
Capza2CAPZA21.6Iqsec1IQSEC12.4
Cntnap1CNTNAP10.5Iqsec2IQSEC22.7Mouse
Cntnap2CNTNAP22.1KalrnKALRN8.3Mouse
Dlg1DLG15.3MouseKcnab2KCNAB24.4
Dlg2DLG26.3MouseKcnq2KCNQ20.9
Dlg3DLG37.5MouseLgi1LGI111Mouse
Dlg4DLG44.9Magi2MAGI20.5
Dlgap1DLGAP13.5MouseNlgn2NLGN24.4
Dlgap2DLGAP28.3MouseNrxn1NRXN11.5
Dlgap3DLGAP38.3MouseNrxn3NRXN33.8Mouse
Dlgap4DLGAP416.6MouseRac1RAC11.7
Gabbr1GABBR15.8Shank2SHANK28.4Mouse
Gabbr2GABBR23.8MouseShank3SHANK36.5Mouse
Gabra1GABRA12.6Syngap1SYNGAP15.9Mouse
GnasGNAS1.1YwhaeYWHAE1
Gria1GRIA16.7YwhahYWHAH0.5Human
Gria2GRIA24.8MouseYwhaqYWHAQ0.6
Filter: 24 entries 1TXTCSVXLS

Supplementary Tables

Supplementary Table 1.
Protein Identifications and Proteomic Data.
Supplementary Table 2a.
PSD protein abundance (all)
Supplementary Table 2b.
PSD protein abundance (enriched in human)
Supplementary Table 2c.
PSD protein abundance (enriched in mouse)
Supplementary Table 2d.
PSD protein abundance (PSD complexes)
Supplementary Table 3a.
Proteins only detected in human PSD
Supplementary Table 3b.
Proteins only detected in mouse PSD
Supplementary Table 4a.
Functional comparison of human and mouse PSD proteins (all)
Supplementary Table 4b.
Functional comparison of human and mouse PSD proteins (consensus)
Supplementary Table 5.
Pathways enriched in human and mouse unique or enriched proteins.
Supplementary Table 6.
GO Biological Process term enrichment in human and mouse unique or enriched proteins.
Supplementary Table 7.
Proteins related to axon guidance or cell morphology.
Supplementary Table 8.
Functional comparison of all PSD proteins identified in human and mouse.
Supplementary Table 9a.
Pathway analysis of all PSD proteins identified in human and mouse.
Supplementary Table 9b.
Pathway analysis summary of all PSD proteins identified in human and mouse.
Supplementary Table 10.
Analysis of dN/dS values from mouse and human PSD proteins.

Supplementary Table 1. Protein Identifications and Proteomic Data.

For each identified protein several identification (ID) numbers from biological databases are given. The number of total and uniquely identified peptides for each replicate is also provided. Proteins found with two or more peptides in all replicates are classified as members of the consensus mouse PSD. Human orthologues to mouse proteins are provided. Data regarding human PSD proteins is from: Bayes A et al. Nat Neurosci. 2011 Jan;14(1):19-21.

Internal IDDetected MouseDetected Human (PMID:21170055)Appr Gene (m)MGI IDAppr Gene (h)HGNC IDEnsembl (m)Ensembl (h)Entrez Gene (m)Entrez Gene (h)Cluster NumberGene (m)Gene (h)IPI (m)UP (m)IPI (h)UP (h)Shared peptidesmPSD 010203mPSD01mPSD02mPSD03Present in 3 replicas (m)Present in 3 replicas (h) (PMID:21170055)
ab16moc_919cAMBIGUOUSAMBIGUOUSCalm3MGI:103249CALM3HGNC:1449ENSMUSG00000019370ENSG0000016001412315808Cluster 451Calm1|Calm2|Calm3CALM1|CALM2|CALM3IPI00761696P62204IPI00386621P62158Shared peptides with CALM1|CALM2|CALM34114
ab16moc_919aAMBIGUOUSAMBIGUOUSCalm1MGI:88251CALM1HGNC:1442ENSMUSG00000001175ENSG0000016001412313801Cluster 451Calm1|Calm2|Calm3CALM1|CALM2|CALM3IPI00761696P62204IPI00386621P62158Shared peptides with CALM1|CALM2|CALM34114
ab16moc_919bAMBIGUOUSAMBIGUOUSCalm2MGI:103250CALM2HGNC:1445ENSMUSG00000036438ENSG0000014393312314805Cluster 451Calm1|Calm2|Calm3CALM1|CALM2|CALM3IPI00761696P62204IPI00386621P62158Shared peptides with CALM1|CALM2|CALM34114
ab16moc_920YESAMBIGUOUSArf3MGI:99432ARF3HGNC:654ENSMUSG00000051853ENSG0000013428711842377Cluster 382Arf3ARF3IPI00221614P61205IPI00215917P61204Shared peptides with ARF14433YESYES
ab16moc_925YESAMBIGUOUSArf1MGI:99431ARF1HGNC:652ENSMUSG00000048076ENSG0000014376111840375Cluster 382Arf1ARF1IPI00221613P84078IPI00215914P84077Shared peptides with ARF34433YESYES
ab16moc_505YESAMBIGUOUSHspa1lMGI:96231HSPA1LHGNC:5234ENSMUSG00000007033ENSG00000204390154823305Cluster 307Hspa1lHSPA1LIPI00133208P16627IPI00301277P34931Shared peptides with Hspa1a|Hspa1b9968YESYES
ab16moc_465aYESAMBIGUOUSHspa1aMGI:96244HSPA1AHGNC:5232ENSMUSG00000067283ENSG000002043891937403303Cluster 307Hspa1a|Hspa1bHSPA1A|HSPA1BIPI00798482Q61696IPI00304925P08107Shared peptides with HSPA1L10969YESYES
ab16moc_465bAMBIGUOUSHspa1bMGI:99517HSPA1BHGNC:5233ENSMUSG00000067284ENSG00000204388155113304Cluster 307Hspa1a|Hspa1bHSPA1A|HSPA1BIPI00798482Q61696IPI00304925P08107Shared peptides with HSPA1L10969YESYES
ab16moc_1868AMBIGUOUSTubg2MGI:2144208TUBG2HGNC:12419ENSMUSG00000045007ENSG0000003704210376827175Cluster 2218TUBG2IPI00299830Q9NRH3Shared peptides with TUBG1
ab16moc_1867AMBIGUOUSTubg1MGI:101834TUBG1HGNC:12417ENSMUSG00000035198ENSG000001314621037337283Cluster 2218TUBG1IPI00295081P23258Shared peptides with TUBG2
ab16moc_1050YESYESMrps36MGI:1913378MRPS36HGNC:16631ENSMUSG00000061474ENSG000001340566612892259Cluster 372Mrps36MRPS36IPI00315808Q9CQX8IPI00020495P829093212
ab16moc_1307YESYESPrr7MGI:3487246PRR7HGNC:28130ENSMUSG00000034686ENSG0000013118843276380758Cluster 1663Prr7PRR7IPI00132812Q3V0I2IPI00152142Q8TB682222YES
ab16moc_1313YESYESUsmg5MGI:1891435USMG5HGNC:30889ENSMUSG00000071528ENSG000001739156647784833Cluster 463Usmg5USMG5IPI00624653Q78IK2IPI00063903Q96IX5222
ab16moc_514YESYESCend1MGI:1929898CEND1HGNC:24153ENSMUSG00000060240ENSG000001845245775451286Cluster 77Cend1CEND1IPI00122826Q9JKC6IPI00295601Q8N1119877YESYES
ab16moc_560YESYESN28178MGI:2140712KIAA1045HGNC:29180ENSMUSG00000078351ENSG0000012273323008523349Cluster 728KIAA1045N28178IPI00647986Q80TL4IPI00414898Q9UPV78373YESYES
ab16moc_597YESYESCcdc127MGI:1914683CCDC127HGNC:30520ENSMUSG00000021578ENSG0000016436667433133957Cluster 512Ccdc127CCDC127IPI00131843Q3TC33IPI00060148Q96BQ58843YES
ab16moc_713YESYESCalcoco1MGI:1914738CALCOCO1HGNC:29306ENSMUSG00000023055ENSG000000128226748857658Cluster 1537Calcoco1CALCOCO1IPI00461826Q5DTX0IPI00011232Q6FI596345YES
ab16moc_931YESYES1810074P20RikMGI:1914740KIAA0776HGNC:23039ENSMUSG00000040359ENSG000000141236749023376Cluster 2090KIAA0776KIAA0776IPI00317684Q8CCJ3IPI00844000O9487444
ab16moc_155YESYESCkap4MGI:2444926CKAP4HGNC:16991ENSMUSG00000046841ENSG0000013602621619710970Cluster 193Ckap4CKAP4IPI00223047Q8BMK4IPI00433214Q6NWZ127241721YESYES
ab16moc_362YESYES2010300C02RikMGI:1919347C2orf55HGNC:33454ENSMUSG00000026090ENSG0000019687272097343990"Cluster 1084, Cluster 2471"2010300C02RikC2ORF55IPI00454053Q6GQT3IPI00410436Q6NV741412114YES
ab16moc_857YESYES2310022B05RikMGI:1916801C1orf198HGNC:25900ENSMUSG00000031983ENSG000001192806955184886"Cluster 831, Cluster 1477"2310022B05RikC1ORF198IPI00225267Q8C3W1IPI00013912Q9H4255225YES
ab16moc_1315YESYESAgpat5MGI:1196345AGPAT5HGNC:20886ENSMUSG00000031467ENSG000001551895212355326Cluster 2049Agpat5AGPAT5IPI00221486Q9D1E8IPI00028491Q9NUQ2221
ab16moc_426YESYESPlcb1MGI:97613PLCB1HGNC:15917ENSMUSG00000051177ENSG000001826211879523236Cluster 595Plcb1PLCB1IPI00468121Q9Z1B3IPI00395561Q9NQ6611684YESYES
ab16moc_831YESYESPlcb4MGI:107464PLCB4HGNC:9059ENSMUSG00000039943ENSG00000101333187985332Cluster 1985Plcb4PLCB4IPI00625848Q8BXH1IPI00014897Q151475423YES
ab16moc_54YESYESCnpMGI:88437CNPHGNC:2158ENSMUSG00000006782ENSG00000173786127991267Cluster 11Cnp1CNPIPI00319602P16330IPI00306667P0954346364040YESYES
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Supplementary Table 2a. PSD protein abundance (all)

Individual and average abundance values (iBAQ) for mouse and human PSD proteins are given. Data was normalized and log2 transformed. Normalization was achieved by dividing abundance data points by its species abundance average. Abundance fold difference was defined as the ratio of mouse to human average abundance values. To measure significant abundance differences between species a Student’s t-test was used. Proteins significantly enriched in one species are shown in separate sheets. The abundance of proteins from the postsynaptic protein complexes shown in figure 1 are also shown in a separate sheet.

Individual and median abundance values (iBAQ) for mouse and human PSD proteins are given. Normalisation was done by dividing abundace by each species abundance median. Abundance fold difference is defined as the ratio of mouse by human normalised abundance values.

Appr Gene (m)MGI IDAppr Gene (h)HGNC IDEnsembl (m)Ensembl (h)human ibaq protein group idmouse ibaq protein group idiBAQ mPSD01 (Log2, normalised)iBAQ mPSD02 (Log2, normalised)iBAQ mPSD03 (Log2, normalised)iBAQ hPSD01 (Log2, normalised)iBAQ hPSD02 (Log2, normalised)iBAQ hPSD03 (Log2, normalised)iBAQ hPSD average (Log2, normalised)iBAQ mPSD average (Log2, normalised)Average fold change (mPSD from hDB/hPSD from mDB)t-test Significant (Perm 0.01)t-test p value
Sept2MGI:97298SEPT2HGNC:7729ENSMUSG00000026276ENSG000001683854852073.3363.1864.1763.6875.1414.5054.4453.5660.5440.1674
Sept3MGI:1345148SEPT3HGNC:10750ENSMUSG00000022456ENSG00000100167185823315.4435.2345.7174.8615.0845.6355.1945.4651.2070.3712
Sept4MGI:1270156SEPT4HGNC:9165ENSMUSG00000020486ENSG0000018101340621701.1930.9781.0110.019-0.254-0.014-0.0831.0612.209+0.0005
Sept5MGI:1195461SEPT5HGNC:9164ENSMUSG00000072214ENSG00000184702230824087.3167.5167.626-1.4261.365-0.138-0.0667.486187.678+0.0007
Sept6MGI:1888939SEPT6HGNC:15848ENSMUSG00000050379ENSG00000125354133711333.2424.8744.8962.7983.5621.9132.7584.3382.9890.0952
Sept7MGI:1335094SEPT7HGNC:1717ENSMUSG00000001833ENSG00000122545102210987.5747.4577.2646.9647.4666.8947.1087.4321.2510.1836
Sept8MGI:894310SEPT8HGNC:16511ENSMUSG00000018398ENSG00000164402212823713.6323.2183.5752.8843.2542.4492.8623.4751.5290.0829
Sept9MGI:1858222SEPT9HGNC:7323ENSMUSG00000059248ENSG00000184640229420832.1962.1972.1252.5993.3032.8982.9342.1720.5900.0208
Sept10MGI:1918110SEPT10HGNC:14349ENSMUSG00000019917ENSG00000186522182813171.6082.8692.417-1.801-0.201-1.419-1.1412.29810.843+0.0048
Sept11MGI:1277214SEPT11HGNC:25589ENSMUSG00000058013ENSG00000138758245618627.7287.1597.4807.9557.9468.1798.0277.4560.6730.0348
1810074P20RikMGI:1914740KIAA0776HGNC:23039ENSMUSG00000040359ENSG00000014123233421141.2071.8991.711-0.702-0.6320.671-0.2211.6063.5470.0206
2400001E08RikMGI:1913758LAMTOR1HGNC:26068ENSMUSG00000030842ENSG0000014935755314210.113-0.713-0.906-0.413-0.142-1.146-0.567-0.5021.0460.8875
2400003C14RikMGI:1919205KIAA0174HGNC:28977ENSMUSG00000031729ENSG00000182149781660.6901.0320.4500.7621.3842.0471.3980.7240.6270.1736
Aak1MGI:1098687AAK1HGNC:19679ENSMUSG00000057230ENSG00000115977242116902.6702.1742.7920.9140.8931.4611.0902.5452.743+0.0054
AarsMGI:2384560AARSHGNC:20ENSMUSG00000031960ENSG0000009086187914902.670-1.091-4.910-0.852-1.116-0.430-0.799-1.1100.8060.8943
Abcd2MGI:1349467ABCD2HGNC:66ENSMUSG00000055782ENSG000001732081071364-0.642-1.128-2.418-0.778-0.382-0.581-0.580-1.3960.5680.2066
Abcd3MGI:1349216ABCD3HGNC:67ENSMUSG00000028127ENSG0000011752894864-1.540-1.040-1.2660.217-0.929-0.275-0.329-1.2820.5170.0581
Abhd16aMGI:99476ABHD16AHGNC:13921ENSMUSG00000007036ENSG000002044271024694-2.434-1.152-2.737-1.349-0.819-0.405-0.858-2.1080.4200.0883
Abi1MGI:104913ABI1HGNC:11320ENSMUSG00000058835ENSG00000136754201119274.3894.8534.9382.5193.3344.3313.3954.7262.5170.0731
Abi2MGI:106913ABI2HGNC:24011ENSMUSG00000026782ENSG00000138443203017342.8293.2603.2131.5942.9883.3152.6323.1001.3830.4389
Ablim1MGI:1194500ABLIM1HGNC:78ENSMUSG00000078103ENSG00000099204177616880.9021.5541.489-0.0621.8601.1440.9811.3151.2610.6061
Ablim2MGI:2385758ABLIM2HGNC:19195ENSMUSG00000029095ENSG0000016399520171136-2.949-1.597-1.847-2.017-0.338-0.640-0.998-2.1310.4560.1627
Ablim3MGI:2442582ABLIM3HGNC:29132ENSMUSG00000032735ENSG0000017321013051989-1.000-0.658-0.596-3.797-2.034-2.183-2.672-0.7513.7850.0294
AbrMGI:107771ABRHGNC:81ENSMUSG00000017631ENSG000001598429621762-2.507-4.425-3.230-3.250-0.571-0.829-1.550-3.3870.2800.1461
Acat1MGI:87870ACAT1HGNC:93ENSMUSG00000032047ENSG00000075239961956-2.814-3.035-1.048-2.587-1.578-3.925-2.697-2.2991.3180.6894
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Supplementary Table 2b. PSD protein abundance (enriched in human)

Individual and average abundance values (iBAQ) for mouse and human PSD proteins are given. Data was normalized and log2 transformed. Normalization was achieved by dividing abundance data points by its species abundance average. Abundance fold difference was defined as the ratio of mouse to human average abundance values. To measure significant abundance differences between species a Student’s t-test was used. Proteins significantly enriched in one species are shown in separate sheets. The abundance of proteins from the postsynaptic protein complexes shown in figure 1 are also shown in a separate sheet.

Individual and median abundance values (iBAQ) for mouse and human PSD proteins are given. Normalisation was done by dividing abundace by each species abundance median. Abundance fold difference is defined as the ratio of mouse by human normalised abundance values.

Appr Gene (m)MGI IDAppr Gene (h)HGNC IDEnsembl (m)Ensembl (h)human ibaq protein group idmouse ibaq protein group idiBAQ mPSD01 (Log2, normalised)iBAQ mPSD02 (Log2, normalised)iBAQ mPSD03 (Log2, normalised)iBAQ hPSD01 (Log2, normalised)iBAQ hPSD02 (Log2, normalised)iBAQ hPSD03 (Log2, normalised)iBAQ hPSD average (Log2, normalised)iBAQ mPSD average (Log2, normalised)Average fold change (mPSD from hDB/hPSD from mDB)t-test Significant (Permutation 0.01)t-test p value
Stxbp1MGI:107363STXBP1HGNC:11444ENSMUSG00000026797ENSG0000013685410981849-2.846-2.331-2.8365.5266.1836.7226.144-2.6710.002+0.0000
VimMGI:98932VIMHGNC:12692ENSMUSG00000026728ENSG0000002602519871156-0.1160.132-0.0195.1776.2755.2955.583-0.0010.021+0.0001
Gdi1MGI:99846GDI1HGNC:4226ENSMUSG00000015291ENSG000002038793571518-2.370-0.363-2.2903.4863.7944.0543.778-1.6740.023+0.0013
GfapMGI:95697GFAPHGNC:4235ENSMUSG00000020932ENSG000001310958182721.6951.6341.8236.2807.5166.8636.8861.7170.028+0.0001
PpiaMGI:97749PPIAHGNC:9253ENSMUSG00000071866ENSG0000019626219942096-1.795-3.107-2.8932.0853.0532.3752.505-2.5980.029+0.0005
Dpysl3MGI:1349762DPYSL3HGNC:3015ENSMUSG00000024501ENSG000001136572369443-4.083-3.283-4.5680.9370.5511.4640.984-3.9780.032+0.0004
MsnMGI:97167MSNHGNC:7373ENSMUSG00000031207ENSG00000147065142691-2.338-2.133-2.7212.0502.7612.1202.311-2.3970.038+0.0001
LdhbMGI:96763LDHBHGNC:6541ENSMUSG00000030246ENSG0000011171614201203-2.648-2.299-3.6362.5221.6761.1841.794-2.8610.040+0.0011
Hspa1aMGI:96244HSPA1AHGNC:5232ENSMUSG00000067283ENSG0000020438917121666-1.911-2.758-1.2972.4472.9342.2092.530-1.9890.044+0.0007
Hspa1bMGI:99517HSPA1BHGNC:5233ENSMUSG00000067284ENSG0000020438817121666-1.911-2.758-1.2972.4472.9342.2092.530-1.9890.044+0.0007
Glipr2MGI:1917770GLIPR2HGNC:18007ENSMUSG00000028480ENSG000001226942451853-0.304-0.957-2.3473.4523.1013.0923.215-1.2030.047+0.0020
Mapre2MGI:106271MAPRE2HGNC:6891ENSMUSG00000024277ENSG0000016697424182383-4.583-2.726-3.0240.9610.3531.5910.969-3.4440.047+0.0029
Vps45MGI:891965VPS45HGNC:14579ENSMUSG00000015747ENSG000001366311100516-2.319-2.146-2.3111.4502.6952.0862.077-2.2590.050+0.0003
Eno2MGI:95394ENO2HGNC:3353ENSMUSG00000004267ENSG0000011167413391617-1.499-3.182-2.3902.5211.4771.8171.938-2.3570.051+0.0017
Aco2MGI:87880ACO2HGNC:118ENSMUSG00000022477ENSG00000100412582240-2.417-1.370-2.3721.8622.7601.6132.078-2.0530.057+0.0011
Uba1MGI:98890UBA1HGNC:12469ENSMUSG00000001924ENSG000001309852198481-2.037-1.669-2.9731.2361.7512.5141.834-2.2260.060+0.0016
Fscn1MGI:1352745FSCN1HGNC:11148ENSMUSG00000029581ENSG0000007561811801682-2.239-2.102-1.8530.6212.7722.3831.925-2.0650.063+0.0040
Plp1MGI:97623PLP1HGNC:9086ENSMUSG00000031425ENSG0000012356014404060.0360.609-0.3533.6073.8704.1683.8820.0970.073+0.0003
Pdia3MGI:95834PDIA3HGNC:4606ENSMUSG00000027248ENSG000001670048091233-3.881-4.253-4.748-0.797-0.357-0.559-0.571-4.2940.076+0.0002
CkbMGI:88407CKBHGNC:1991ENSMUSG00000001270ENSG000001661657328892.3553.0963.5266.2456.1766.9656.4622.9920.090+0.0012
Ube2v2MGI:1917870UBE2V2HGNC:12495ENSMUSG00000022674ENSG000001691396221782-0.1970.273-0.6573.3382.9183.5503.269-0.1940.091+0.0004
Pip4k2aMGI:1298206PIP4K2AHGNC:8997ENSMUSG00000026737ENSG00000150867338229-0.253-0.522-0.0013.5392.4403.6193.199-0.2590.091+0.0011
Pacsin1MGI:1345181PACSIN1HGNC:8570ENSMUSG00000040276ENSG00000124507404493-0.664-1.285-0.7781.7042.5813.1702.485-0.9090.095+0.0019
Rras2MGI:1914172RRAS2HGNC:17271ENSMUSG00000055723ENSG000001338184321534-1.115-1.052-1.9262.3291.1612.1941.895-1.3640.104+0.0022
Lrrc47MGI:1920196LRRC47HGNC:29207ENSMUSG00000029028ENSG000001307641224917-5.811-4.686-4.074-2.047-1.352-1.625-1.675-4.8570.110+0.0044
Filter: 69 entries 123TXTCSVXLS

Supplementary Table 2c. PSD protein abundance (enriched in mouse)

Individual and average abundance values (iBAQ) for mouse and human PSD proteins are given. Data was normalized and log2 transformed. Normalization was achieved by dividing abundance data points by its species abundance average. Abundance fold difference was defined as the ratio of mouse to human average abundance values. To measure significant abundance differences between species a Student’s t-test was used. Proteins significantly enriched in one species are shown in separate sheets. The abundance of proteins from the postsynaptic protein complexes shown in figure 1 are also shown in a separate sheet.

Individual and median abundance values (iBAQ) for mouse and human PSD proteins are given. Normalisation was done by dividing abundace by each species abundance median. Abundance fold difference is defined as the ratio of mouse by human normalised abundance values.

Appr Gene (m)MGI IDAppr Gene (h)HGNC IDEnsembl (m)Ensembl (h)human ibaq protein group idmouse ibaq protein group idiBAQ mPSD01 (Log2, normalised)iBAQ mPSD02 (Log2, normalised)iBAQ mPSD03 (Log2, normalised)iBAQ hPSD01 (Log2, normalised)iBAQ hPSD02 (Log2, normalised)iBAQ hPSD03 (Log2, normalised)iBAQ hPSD average (Log2, normalised)iBAQ mPSD average (Log2, normalised)Average fold change (mPSD from hDB/hPSD from mDB)t-test Significant (Permutation 0.01)t-test p value
Sept5MGI:1195461SEPT5HGNC:9164ENSMUSG00000072214ENSG00000184702230824087.3167.5167.626-1.4261.365-0.138-0.0667.486187.678+0.0007
Cacna2d3MGI:1338890CACNA2D3HGNC:15460ENSMUSG00000021991ENSG0000015744516876891.3650.6480.570-3.585-4.646-6.482-4.9050.86154.406+0.0028
Mdh1MGI:97051MDH1HGNC:6970ENSMUSG00000020321ENSG00000014641242016227.5575.8777.4262.4171.9930.5871.6666.95339.060+0.0024
Camk2gMGI:88259CAMK2GHGNC:1463ENSMUSG00000021820ENSG0000014866024035262.7473.7483.277-2.436-2.479-0.822-1.9133.25736.001+0.0011
Gria4MGI:95811GRIA4HGNC:4574ENSMUSG00000025892ENSG0000015257822297400.3720.5371.152-4.956-3.320-3.386-3.8870.68723.829+0.0014
Dbn1MGI:1931838DBN1HGNC:2695ENSMUSG00000034675ENSG0000011375823188584.0263.9294.859-0.9700.726-0.340-0.1954.27122.101+0.0015
Anks1bMGI:1924781ANKS1BHGNC:24600ENSMUSG00000058589ENSG00000185046204222055.5265.9415.5930.7401.6731.6881.3675.68719.975+0.0002
Dlgap4MGI:2138865DLGAP4HGNC:24476ENSMUSG00000061689ENSG0000008084525322491.4251.2991.402-1.971-2.190-3.878-2.6801.37516.621+0.0026
Mal2MGI:2146021MAL2HGNC:13634ENSMUSG00000024479ENSG00000147676105610364.9805.1225.3020.7422.1500.7511.2145.13515.140+0.0012
Rpl6MGI:108057RPL6HGNC:10362ENSMUSG00000029614ENSG00000089009177514011.1210.0510.614-2.119-3.970-3.098-3.0620.59512.616+0.0041
D3Bwg0562eMGI:106530NOT_FOUNDNOT_FOUNDENSMUSG00000044667ENSG00000117600181818701.7971.4591.301-2.533-1.840-1.690-2.0211.51911.631+0.0003
Shisa7MGI:3605641SHISA7HGNC:35409ENSMUSG00000053550ENSG00000187902242223771.9962.3932.150-2.083-0.354-1.425-1.2872.18011.056+0.0026
Lgi1MGI:1861691LGI1HGNC:6572ENSMUSG00000067242ENSG000001082316613841.6072.3442.308-1.292-2.008-0.797-1.3662.08610.943+0.0013
Sept10MGI:1918110SEPT10HGNC:14349ENSMUSG00000019917ENSG00000186522182813171.6082.8692.417-1.801-0.201-1.419-1.1412.29810.843+0.0048
BegainMGI:3044626BEGAINHGNC:24163ENSMUSG00000040867ENSG0000018309238617320.7081.3200.943-2.243-1.662-3.271-2.3920.99110.430+0.0025
Ppfia4MGI:1915757PPFIA4HGNC:9248ENSMUSG00000026458ENSG00000143847218324060.7130.6730.462-2.257-3.308-2.397-2.6540.6169.645+0.0006
PuraMGI:103079PURAHGNC:9701ENSMUSG00000043991ENSG000001851297543124.8914.6004.7911.2751.3812.0421.5664.7609.156+0.0002
Shank2MGI:2671987SHANK2HGNC:14295ENSMUSG00000037541ENSG00000162105235716733.1882.7733.377-0.4120.4320.0810.0343.1138.450+0.0005
Sh3pxd2aMGI:1298393SH3PXD2AHGNC:23664ENSMUSG00000053617ENSG0000010795719241329-2.363-2.577-2.296-5.278-6.411-4.737-5.475-2.4128.359+0.0036
Dlgap2MGI:2443181DLGAP2HGNC:2906ENSMUSG00000047495ENSG00000198010102510451.7731.9971.976-1.389-0.682-1.366-1.1451.9168.345+0.0002
Dlgap3MGI:3039563DLGAP3HGNC:30368ENSMUSG00000042388ENSG0000011654414298473.0113.3353.164-0.4260.5530.2040.1103.1708.339+0.0005
KalrnMGI:2685385KALRNHGNC:4814ENSMUSG00000061751ENSG0000016014590921191.1270.8651.453-2.497-0.952-2.262-1.9041.1488.293+0.0039
Dpp6MGI:94921DPP6HGNC:3010ENSMUSG00000061576ENSG0000013022615202378-1.423-1.620-0.973-4.494-4.200-4.371-4.355-1.3388.091+0.0001
Grin1MGI:95819GRIN1HGNC:4584ENSMUSG00000026959ENSG00000176884209022473.4123.6953.018-0.0850.5030.8910.4373.3757.666+0.0010
Rimbp2MGI:2443235RIMBP2HGNC:30339ENSMUSG00000029420ENSG00000060709129023250.6470.4460.292-2.149-2.088-3.116-2.4510.4627.528+0.0011
Filter: 87 entries 1234TXTCSVXLS

Supplementary Table 2d. PSD protein abundance (PSD complexes)

Individual and average abundance values (iBAQ) for mouse and human PSD proteins are given. Data was normalized and log2 transformed. Normalization was achieved by dividing abundance data points by its species abundance average. Abundance fold difference was defined as the ratio of mouse to human average abundance values. To measure significant abundance differences between species a Student’s t-test was used. Proteins significantly enriched in one species are shown in separate sheets. The abundance of proteins from the postsynaptic protein complexes shown in figure 1 are also shown in a separate sheet.

Individual and median abundance values (iBAQ) for mouse and human PSD proteins are given. Normalisation was done by dividing abundace by each species abundance median. Abundance fold difference is defined as the ratio of mouse by human normalised abundance values.

MGI IDAppr Gene (h)PSD95 ComplexNR ComplexmGluR5 Complexhuman ibaq protein group idmouse ibaq protein group idiBAQ mPSD01 (Log2, normalised)iBAQ mPSD02 (Log2, normalised)iBAQ mPSD03 (Log2, normalised)iBAQ hPSD01 (Log2, normalised)iBAQ hPSD02 (Log2, normalised)iBAQ hPSD03 (Log2, normalised)iBAQ hPSD average (Log2, normalised)iBAQ mPSD average (Log2, normalised)Average fold change (mPSD from hDB/hPSD from mDB)t-test Significant (Perm 0.01)t-test p value
MGI:95820GRIN2AYESYESYES9513091.0270.9531.121-1.310-1.009-1.563-1.2941.0345.020+0.000
MGI:104560NSFYESYESYES22221903.0514.0663.7713.3614.8064.1634.1103.6290.7170.404
MGI:2388633CLTCYESYESYES7679824.5403.5924.0053.9705.2064.6834.6204.0460.6720.272
MGI:1353495SLC25A4YESYESNO729219-0.786-2.634-4.7333.2942.6461.8632.601-2.7180.0250.012
MGI:99432ARF3YESYESNO13211026-0.599-2.604-5.0610.7560.564-1.2150.035-2.7550.1450.124
MGI:107363STXBP1YESYESNO10981849-2.846-2.331-2.8365.5266.1836.7226.144-2.6710.002+0.000
MGI:87880ACO2YESYESNO582240-2.417-1.370-2.3721.8622.7601.6132.078-2.0530.057+0.001
MGI:1346858MAPK1YESYESNO-1.803-1.043-2.2320.992-0.6702.1960.839-1.6930.173
MGI:99523PRDX1YESYESNO60427-1.416-0.599-0.6771.3351.851-0.9860.733-0.8970.3230.148
MGI:1316660CACNG2YESYESNO82783-0.456-0.2670.385-0.950-2.174-1.317-1.481-0.1132.5810.037
MGI:97623PLP1YESYESNO14404060.0360.609-0.3533.6073.8704.1683.8820.0970.073+0.000
MGI:1915339ARPC4YESYESNO21559260.7430.3210.0830.5341.201-0.4310.4350.3820.9640.923
MGI:101931SLC1A2YESYESNO167220581.9991.4420.701-0.287-0.4560.228-0.1721.3802.9320.022
MGI:1194500ABLIM1YESYESNO177616880.9021.5541.489-0.0621.8601.1440.9811.3151.2610.606
MGI:2685385KALRNYESYESNO90921191.1270.8651.453-2.497-0.952-2.262-1.9041.1488.293+0.004
MGI:107164PPP3CAYESYESNO12714211.7322.0671.5211.8242.0692.4552.1161.7730.7890.231
MGI:102520PHB2YESYESNO86814982.7542.2791.4553.7103.1091.9942.9382.1630.5840.286
MGI:1861691LGI1YESYESNO6613841.6072.3442.308-1.292-2.008-0.797-1.3662.08610.943+0.001
MGI:95739GLULYESYESNO35421502.5073.0412.6072.7631.8651.2641.9642.7191.6870.180
MGI:1346065DLGAP1YESYESNO69121692.6063.0203.2701.1891.6260.6881.1672.9653.477+0.006
MGI:95821GRIN2BYESYESNO163914912.9912.9923.007-1.2010.7070.7580.0882.9967.5070.011
MGI:107231DLG1YESYESNO95918343.0162.8712.8390.4330.3550.7340.5072.9095.282+0.000
MGI:1353496SLC25A5YESYESNO2576084.1223.5842.3370.979-0.645-1.403-0.3563.34813.0340.014
MGI:95819GRIN1YESYESNO209022473.4123.6953.018-0.0850.5030.8910.4373.3757.666+0.001
MGI:95640GAPDHYESYESNO140813103.3783.4003.4803.8733.8074.6434.1083.4190.6200.063
Filter: 831 entries 123...34TXTCSVXLS

Supplementary Table 3a. Proteins only detected in human PSD

Proteins only found in human or mouse are shown in separate sheets. For each protein several identification (ID) numbers from biological databases are given.

For each identified protein several identification (ID) numbers from biological databases are given.

Internal IDAppr GeneHGNC IDEnsemblEntrez GeneUPMGI IDEnsembl (mouse)Present in 3 replicas
ab16moc_1596C10orf35HGNC:23519ENSG00000171224219738Q96D05MGI:1917144ENSMUSG00000020083YES
ab16moc_1558ACO2HGNC:118ENSG0000010041250Q99798MGI:87880ENSMUSG00000022477YES
ab16moc_1658AK5HGNC:365ENSG0000015402726289Q5U622MGI:2677491ENSMUSG00000039058YES
ab16moc_1712AK1HGNC:361ENSG00000106992203Q53EY8MGI:87977ENSMUSG00000026817YES
ab16moc_1563CAP2HGNC:20039ENSG0000011218610486P40123MGI:1914502ENSMUSG00000021373YES
ab16moc_1642AHNAKHGNC:347ENSG0000012494279026Q09666MGI:1316648ENSMUSG00000069833YES
ab16moc_1686ALDH2HGNC:404ENSG00000111275217P05091MGI:99600ENSMUSG00000029455YES
ab16moc_1727ALDH7A1HGNC:877ENSG00000164904501P49419MGI:108186ENSMUSG00000053644YES
ab16moc_1681AKR1A1HGNC:380ENSG0000011744810327P14550MGI:1929955ENSMUSG00000028692YES
ab16moc_1754AKR7A2HGNC:389ENSG000000533718574O43488MGI:107796ENSMUSG00000028743YES
ab16moc_1745SNTA1HGNC:11167ENSG000001014006640Q13424MGI:101772ENSMUSG00000027488YES
ab16moc_1660CRYABHGNC:2389ENSG000001098461410P02511MGI:88516ENSMUSG00000032060YES
ab16moc_1647ANXA2HGNC:537ENSG00000182718302P07355MGI:88246ENSMUSG00000032231YES
ab16moc_1663ANXA5HGNC:543ENSG00000164111308P08758MGI:106008ENSMUSG00000027712YES
ab16moc_1643ANXA6HGNC:544ENSG00000197043309P08133MGI:88255ENSMUSG00000018340YES
ab16moc_1796APODHGNC:612ENSG00000189058347P05090MGI:88056ENSMUSG00000022548YES
ab16moc_1724APOL2HGNC:619ENSG0000010033623780Q9BQE5MGI:2444921ENSMUSG00000056656YES
ab16moc_1646PRKDCHGNC:9413ENSG000001210315591P78527MGI:104779ENSMUSG00000022672YES
ab16moc_1574ATL1HGNC:11231ENSG0000019851351602Q8WXF7MGI:1921241ENSMUSG00000021066YES
ab16moc_1870BAG3HGNC:939ENSG000001519299531O95817MGI:1352493ENSMUSG00000030847YES
ab16moc_1790SNTB2HGNC:11169ENSG000001688076645Q13425MGI:101771ENSMUSG00000041308YES
ab16moc_1750CA2HGNC:1373ENSG00000104267760P00918MGI:88269ENSMUSG00000027562YES
ab16moc_1797CST3HGNC:2475ENSG000001703731471P01034MGI:102519ENSMUSG00000027447YES
ab16moc_1873CYBRD1HGNC:20797ENSG0000007196779901Q53TN4MGI:2654575ENSMUSG00000027015YES
ab16moc_1614DYNLRB1HGNC:15468ENSG0000012597183658Q9NP97MGI:1914318ENSMUSG00000047459YES
Filter: 442 entries 123...18TXTCSVXLS

Supplementary Table 3b. Proteins only detected in mouse PSD

Proteins only found in human or mouse are shown in separate sheets. For each protein several identification (ID) numbers from biological databases are given.

For each identified protein several identification (ID) numbers from biological databases are given.

Internal IDAppr GeneMGI IDEnsemblEntrez GeneUPHGNC IDEnsembl (h)Present in 3 replicas
ab16moc_1009Fam171a2MGI:2448496ENSMUSG00000034685217219A2A699HGNC:30480ENSG00000161682YES
ab16moc_1433Tmem163MGI:1919410ENSMUSG0000002634772160Q8C996HGNC:25380ENSG00000152128YES
ab16moc_285Fam126bMGI:1098784ENSMUSG00000038174213056Q3UMY7HGNC:28593ENSG00000155744YES
ab16moc_6109430020K01RikMGI:2685174ENSMUSG00000033960240185Q5DTX6HGNC:29283ENSG00000165757YES
ab16moc_748NclnMGI:1926081ENSMUSG00000020238103425Q8VCM8HGNC:26923ENSG00000125912YES
ab16moc_11496720456B07RikMGI:1915406ENSMUSG00000033940101314Q91VR8HGNC:23057ENSG00000219870YES
ab16moc_124Tubb5MGI:107812ENSMUSG0000000152522154P99024HGNC:20778ENSG00000196230YES
ab16moc_8541700054N08RikMGI:1920670ENSMUSG0000003197173420Q8QZT2HGNC:29578ENSG00000154429YES
ab16moc_834Rpl11MGI:1914275ENSMUSG0000005929167025Q9CXW4HGNC:10301ENSG00000142676YES
ab16moc_836Rpl19MGI:98020ENSMUSG0000001740419921A2A547HGNC:10312ENSG00000108298YES
ab16moc_674Rpl26MGI:106022ENSMUSG0000006093819941P61255HGNC:10327ENSG00000161970YES
ab16moc_850Rpl27MGI:98036ENSMUSG0000006331619942P61358HGNC:10328ENSG00000131469YES
ab16moc_607Rpl28MGI:101839ENSMUSG0000003043219943P41105HGNC:10330ENSG00000108107YES
ab16moc_1178Rpl31MGI:2149632ENSMUSG00000073702114641P62900HGNC:10334ENSG00000071082YES
ab16moc_997Rpl32MGI:98038ENSMUSG0000005784119951P62911HGNC:10336ENSG00000144713YES
ab16moc_745Rpl34MGI:1915686ENSMUSG0000006200668436Q9D1R9HGNC:10340ENSG00000109475YES
ab16moc_422Akap2MGI:1306795ENSMUSG0000003872911641A2AKL6HGNC:372ENSG00000157654YES
ab16moc_993Adam11MGI:1098667ENSMUSG0000002092611488Q9R1V4HGNC:189ENSG00000073670YES
ab16moc_1014AlplMGI:87983ENSMUSG0000002876611647P09242HGNC:438ENSG00000162551YES
ab16moc_839Aifm1MGI:1349419ENSMUSG0000003693226926Q9Z0X1HGNC:8768ENSG00000156709YES
ab16moc_853Arfgap3MGI:1913501ENSMUSG0000005427766251Q9D8S3HGNC:661ENSG00000100262YES
ab16moc_361ArvcfMGI:109620ENSMUSG0000000032511877P98203HGNC:728ENSG00000099889YES
ab16moc_843Abcd2MGI:1349467ENSMUSG0000005578226874Q61285HGNC:66ENSG00000173208YES
ab16moc_880Bai2MGI:2451244ENSMUSG00000028782230775Q8CGM1HGNC:944ENSG00000121753YES
ab16moc_671Prkar1bMGI:97759ENSMUSG0000002585519085P12849HGNC:9390ENSG00000188191YES
Filter: 537 entries 123...22TXTCSVXLS

Supplementary Table 4a. All PSD

Proteins from the total PSD exclusive to human or mouse were classified independently using the Panther 'Protein Class' descriptor. Enrichment analysis was done to determine Protein Classes overrepresented in each species set of exclusive molecules. The Benjamini-Hochberg procedure was used to correct for multiple testing. The column 'observed' retrieves the number of proteins identified in each 'Protein Class' while the column 'expected', the number that would have been identified by chance. Over or under-representations are shown by a (+) or (-) symbol respectively. A second sheet contains the same analysis but done only for the molecules from the consensus PSD.

Human and mouse PSD proteins not found in the other specie were classified independenly using the Panther 'Protein Class' descriptor. An enrichment analysis was done to determine Protein Classes overrepresented in each species as compared with the human genome. P-values were corrected for multiple testing using the Benjamini-Hochberg procedure. The colum 'observed' retrives the number of proteins identified in each 'Protein Class' while the column 'expected', the number which would have been identified by chance. Over or underrepresntations are shown by a (+) or (-) symbol respectively.

Protein classes in human PSD as compared with human genome Protein classes in mouse PSD as compared with human genome
PANTHER Protein ClassHomo sapiens genesObservedExpectedover/underCorrected P-valueObservedExpectedover/underP-valueCorrected P-value
cytoskeletal protein441369.17+1.30E-091410.85+2.03E-016.18E-01
oxidoreductase5503911.44+5.20E-092413.54+5.68E-035.22E-02
transcription factor2067942.98-5.26E-091150.87-2.59E-121.67E-10
transferase15127031.44+1.44E-084037.21+3.41E-017.86E-01
dehydrogenase210224.37+4.52E-08135.17+2.51E-033.22E-02
membrane traffic protein321276.67+4.74E-08187.9+1.26E-032.03E-02
membrane trafficking regulatory protein107162.22+4.74E-0842.63+2.71E-017.42E-01
actin family cytoskeletal protein222224.62+7.62E-0865.46+4.65E-018.19E-01
kinase6794014.12+1.25E-072516.71+3.20E-021.82E-01
nucleotide kinase51101.06+3.36E-0641.26+3.85E-022.12E-01
non-motor actin binding protein114142.37+3.39E-0622.81-4.68E-018.19E-01
zinc finger transcription factor803116.7-1.17E-05319.76-2.92E-067.04E-05
Unclassified6763104140.62-9.26E-04162166.43-3.55E-018.03E-01
reductase6581.35+1.10E-0351.6+2.34E-021.51E-01
protein kinase5102510.6+1.15E-031612.55+1.95E-016.13E-01
KRAB box transcription factor552111.48-1.36E-03013.58-1.04E-062.87E-05
microtubule family cytoskeletal protein156113.24+5.89E-0363.84+1.90E-016.13E-01
enzyme modulator8573317.82+6.53E-033421.09+4.89E-034.97E-02
transfer/carrier protein248145.16+8.54E-0336.1-1.41E-015.04E-01
G-protein modulator278155.78+8.54E-03166.84+1.77E-032.58E-02
transaminase2540.52+1.83E-0200.62-5.40E-018.19E-01
peroxidase2740.56+2.31E-0200.66-5.14E-018.19E-01
G-protein206114.28+3.74E-0275.07+2.47E-017.12E-01
ion channel34117.09-5.18E-02318.39+9.63E-103.72E-08
acetyltransferase10572.18+5.40E-0232.58+4.78E-018.19E-01
aminoacyl-tRNA synthetase2030.42+6.50E-0210.49+3.89E-018.19E-01
ligase260125.41+6.60E-02106.4+1.13E-014.54E-01
isomerase9461.95+1.01E-0102.31-9.84E-024.13E-01
small GTPase15883.29+1.25E-0163.89+1.97E-016.13E-01
chaperone13072.7+1.25E-0123.2-3.79E-018.19E-01
transaldolase110.02+1.25E-0100.02-9.76E-011.00E+00
receptor10761322.37-1.25E-013426.48+8.40E-023.85E-01
lyase10462.16+1.33E-0152.56+1.16E-014.57E-01
mRNA processing factor17903.72-1.35E-01114.41+5.50E-035.22E-02
vesicle coat protein3030.62+1.38E-0110.74+5.22E-018.19E-01
non-motor microtubule binding protein5341.1+1.38E-0141.3+4.33E-022.23E-01
dehydratase3130.64+1.44E-0100.76-4.66E-018.19E-01
phosphorylase1320.27+1.52E-0100.32-7.26E-018.87E-01
transcription cofactor25515.3-1.52E-0136.28-1.27E-014.84E-01
transmembrane receptor regulatory/adaptor protein8451.75+1.56E-0112.07-3.88E-018.19E-01
G-protein coupled receptor44749.29-2.08E-011311+3.10E-017.86E-01
antibacterial response protein1820.37+2.49E-0100.44-6.42E-018.60E-01
hydrolase454159.44+2.49E-011211.17+4.42E-018.19E-01
nucleic acid binding14662230.48-2.70E-017836.08+1.38E-106.66E-09
basic helix-loop-helix transcription factor12002.5-3.51E-0112.95-2.05E-016.18E-01
guanyl-nucleotide exchange factor7941.64+3.54E-0131.94+3.08E-017.86E-01
tubulin2520.52+3.95E-0110.62+4.60E-018.19E-01
transketolase510.1+3.97E-0100.12-8.84E-019.69E-01
phosphodiesterase2720.56+4.25E-0130.66+2.99E-021.79E-01
cysteine protease12152.52+4.25E-0122.98-4.28E-018.19E-01
kinase modulator10302.14-4.43E-0162.53+4.39E-022.23E-01
lipase5731.19+4.43E-0131.4+1.67E-015.65E-01
ligand-gated ion channel10102.1-4.44E-01112.49+5.47E-059.60E-04
peptide hormone16913.51-4.70E-0134.16-4.02E-018.19E-01
DNA binding protein47669.9-4.70E-011111.71-4.94E-018.19E-01
homeobox transcription factor23324.84-4.72E-0105.73-3.13E-033.55E-02
helix-turn-helix transcription factor23324.84-4.72E-0105.73-3.13E-033.55E-02
amino acid transporter9842.04+4.96E-0132.41+4.34E-018.19E-01
potassium channel8901.85-5.14E-0182.19+1.87E-032.58E-02
actin binding motor protein910.19+5.47E-0100.22-8.01E-019.37E-01
heterotrimeric G-protein3620.75+5.47E-0110.89+5.88E-018.20E-01
phospholipase3620.75+5.47E-0130.89+6.04E-022.84E-01
cytokine receptor21324.43-5.51E-0165.24+4.27E-018.19E-01
intermediate filament binding protein1010.21+5.67E-0120.25+2.57E-021.60E-01
Hsp90 family chaperone1010.21+5.67E-0100.25-7.82E-019.26E-01
chromatin/chromatin-binding protein7431.54+5.85E-0121.82+5.44E-018.19E-01
intermediate filament1110.23+5.85E-0120.27+3.06E-021.79E-01
phosphatase23074.78+5.85E-0185.66+2.10E-016.23E-01
Hsp70 family chaperone1310.27+6.63E-0100.32-7.26E-018.87E-01
cell junction protein6701.39-6.78E-0101.65-1.92E-016.13E-01
microtubule binding motor protein4620.96+6.78E-0111.13-6.87E-018.70E-01
mutase1410.29+6.78E-0100.34-7.08E-018.70E-01
RNA binding protein7271215.12-6.78E-016017.89+6.16E-161.19E-13
glucosidase1510.31+6.83E-0100.37-6.91E-018.70E-01
storage protein1510.31+6.83E-0100.37-6.91E-018.70E-01
calcium-binding protein6301.31-6.83E-0111.55-5.41E-018.19E-01
acyltransferase8831.83+6.94E-0112.17-3.62E-018.03E-01
cation transporter17823.7-6.99E-0174.38+1.53E-015.37E-01
methyltransferase13042.7+6.99E-0123.2-3.79E-018.19E-01
ubiquitin-protein ligase13242.74+7.04E-0163.25+1.10E-014.52E-01
DNA methyltransferase1710.35+7.04E-0100.42-6.58E-018.70E-01
glycosyltransferase22934.76-7.04E-0165.64+4.95E-018.19E-01
translation factor5621.16+7.56E-0151.38+1.33E-029.51E-02
histone5401.12-7.56E-0151.33+1.15E-028.54E-02
chaperonin2010.42+7.72E-0100.49-6.11E-018.30E-01
signaling molecule9612219.98+7.85E-012323.65-5.00E-018.19E-01
cysteine protease inhibitor2110.44+7.85E-0100.52-5.96E-018.20E-01
structural protein28075.82+8.00E-01106.89+1.57E-015.41E-01
immunoglobulin receptor superfamily15523.22-8.00E-0153.81+3.35E-017.86E-01
replication origin binding protein4700.98-8.00E-0121.16+3.22E-017.86E-01
phosphatase modulator6321.31+8.00E-0111.55-5.41E-018.19E-01
nuclear hormone receptor4600.96-8.05E-0111.13-6.87E-018.70E-01
defense/immunity protein10732.22+8.05E-0112.63-2.60E-017.27E-01
kinase activator4500.94-8.05E-0121.11+3.04E-017.86E-01
damaged DNA-binding protein4500.94-8.05E-0101.11-3.30E-017.86E-01
esterase2510.52+8.16E-0100.62-5.40E-018.19E-01
protein phosphatase11132.31+8.16E-0132.73+5.15E-018.19E-01
cell adhesion molecule9311.93-8.35E-0122.29-5.99E-018.20E-01
transporter10982422.83+8.38E-015727.02+1.27E-074.09E-06
phosphatase inhibitor2810.58+8.48E-0100.69-5.02E-018.19E-01
growth factor16543.43+8.48E-0114.06-8.64E-023.85E-01
actin and actin related protein3110.64+8.48E-0110.76+5.34E-018.19E-01
membrane-bound signaling molecule13322.77-8.48E-0133.27-5.86E-018.20E-01
nucleotidyltransferase8411.75-8.48E-0122.07-6.58E-018.70E-01
nucleotide phosphatase3500.73-8.48E-0130.86+5.65E-022.73E-01
DNA helicase8021.66+8.48E-0101.97-1.39E-015.04E-01
immunoglobulin3310.69+8.48E-0100.81-4.44E-018.19E-01
intracellular calcium-sensing protein3300.69-8.48E-0110.81+5.56E-018.19E-01
endoribonuclease3300.69-8.48E-0100.81-4.44E-018.19E-01
calmodulin3300.69-8.48E-0110.81+5.56E-018.19E-01
myelin protein3300.69-8.48E-0140.81+9.48E-037.35E-02
serine protease inhibitor7911.64-8.48E-0111.94-4.21E-018.19E-01
carbohydrate kinase3510.73+8.48E-0100.86-4.22E-018.19E-01
nuclease3510.73+8.48E-0120.86+2.13E-016.23E-01
calcium channel3100.64-8.48E-0170.76+1.48E-052.86E-04
type I cytokine receptor3100.64-8.48E-0110.76+5.34E-018.19E-01
interleukin superfamily3610.75+8.48E-0100.89-4.12E-018.19E-01
protease476109.9+8.48E-01611.71-5.16E-022.55E-01
ribosomal protein18443.83+8.48E-01294.53+8.24E-157.95E-13
tight junction3000.62-8.48E-0100.74-4.78E-018.19E-01
anion channel3710.77+8.48E-0110.91+5.98E-018.20E-01
SNARE protein3710.77+8.48E-0180.91+5.01E-061.07E-04
oxygenase7411.54-8.48E-0121.82+5.44E-018.19E-01
ATP-binding cassette (ABC) transporter7411.54-8.48E-0121.82+5.44E-018.19E-01
major histocompatibility complex antigen2800.58-8.48E-0110.69+4.98E-018.19E-01
neuropeptide2800.58-8.48E-0100.69-5.02E-018.19E-01
extracellular matrix protein7211.5-8.48E-0161.77+9.52E-037.35E-02
RNA helicase7111.48-8.48E-0161.75+8.93E-037.35E-02
cytokine15933.31-8.48E-0113.91-9.73E-024.13E-01
glycosidase2600.54-8.48E-0100.64-5.27E-018.19E-01
apolipoprotein4210.87+8.48E-0101.03-3.55E-018.03E-01
immunoglobulin superfamily cell adhesion molecule2500.52-8.48E-0110.62+4.60E-018.19E-01
hydroxylase4410.91+8.48E-0101.08-3.38E-017.86E-01
HMG box transcription factor4410.91+8.48E-0101.08-3.38E-017.86E-01
protease inhibitor10922.27-8.48E-0112.68-2.51E-017.12E-01
serine protease15333.18-8.48E-0123.77-2.73E-017.42E-01
exoribonuclease2400.5-8.48E-0100.59-5.54E-018.19E-01
basic leucine zipper transcription factor2400.5-8.48E-0100.59-5.54E-018.19E-01
CREB transcription factor2400.5-8.48E-0100.59-5.54E-018.19E-01
carbohydrate transporter4610.96+8.48E-0101.13-3.22E-017.86E-01
cyclase2300.48-8.48E-0130.57+1.98E-021.32E-01
chemokine4811+8.48E-0101.18-3.06E-017.86E-01
tumor necrosis factor receptor2200.46-8.48E-0100.54-5.82E-018.20E-01
RNA methyltransferase2200.46-8.48E-0100.54-5.82E-018.20E-01
ribonucleoprotein6111.27-8.48E-0131.5+1.91E-016.13E-01
metalloprotease14533.01-8.48E-0113.57-1.28E-014.84E-01
gap junction2100.44-8.48E-0100.52-5.96E-018.20E-01
adenylate cyclase2100.44-8.48E-0130.52+1.56E-021.08E-01
endodeoxyribonuclease2000.42-8.54E-0100.49-6.11E-018.30E-01
sodium channel2000.42-8.54E-0120.49+8.78E-023.85E-01
oxidase5711.19-8.54E-0111.4-5.91E-018.20E-01
extracellular matrix glycoprotein5511.14-8.67E-0161.35+2.67E-033.22E-02
centromere DNA-binding protein1800.37-8.68E-0100.44-6.42E-018.60E-01
mitochondrial carrier protein1700.35-8.76E-0130.42+8.91E-037.35E-02
interferon superfamily1700.35-8.76E-0100.42-6.58E-018.70E-01
decarboxylase1700.35-8.76E-0110.42+3.42E-017.86E-01
ATP synthase5111.06-8.76E-0141.26+3.85E-022.12E-01
galactosidase1600.33-8.76E-0100.39-6.74E-018.70E-01
kinase inhibitor1500.31-8.89E-0100.37-6.91E-018.70E-01
surfactant1500.31-8.89E-0100.37-6.91E-018.70E-01
DNA-directed RNA polymerase1500.31-8.89E-0100.37-6.91E-018.70E-01
aspartic protease1400.29-8.90E-0110.34+2.92E-017.83E-01
deaminase1200.25-9.22E-0100.3-7.44E-018.97E-01
DNA glycosylase1200.25-9.22E-0100.3-7.44E-018.97E-01
tumor necrosis factor family member1100.23-9.31E-0100.27-7.63E-019.09E-01
DNA-directed DNA polymerase1000.21-9.44E-0100.25-7.82E-019.26E-01
extracellular matrix structural protein900.19-9.58E-0100.22-8.01E-019.37E-01
carbohydrate phosphatase900.19-9.58E-0100.22-8.01E-019.37E-01
annexin900.19-9.58E-0100.22-8.01E-019.37E-01
protein kinase receptor800.17-9.62E-0100.2-8.21E-019.38E-01
neurotrophic factor800.17-9.62E-0100.2-8.21E-019.38E-01
epimerase/racemase700.15-9.68E-0100.17-8.42E-019.50E-01
viral protein700.15-9.68E-0100.17-8.42E-019.50E-01
viral coat protein700.15-9.68E-0100.17-8.42E-019.50E-01
DNA strand-pairing protein700.15-9.68E-0100.17-8.42E-019.50E-01
amylase600.12-9.68E-0100.15-8.63E-019.52E-01
DNA ligase600.12-9.68E-0110.15+1.37E-015.04E-01
helicase500.1-9.77E-0100.12-8.84E-019.69E-01
amino acid kinase500.1-9.77E-0100.12-8.84E-019.69E-01
pyrophosphatase500.1-9.77E-0100.12-8.84E-019.69E-01
metalloprotease inhibitor400.08-9.81E-0100.1-9.06E-019.71E-01
aldolase400.08-9.81E-0100.1-9.06E-019.71E-01
DNA topoisomerase400.08-9.81E-0100.1-9.06E-019.71E-01
deacetylase200.04-1.00E+0000.05-9.52E-011.00E+00
calsequestrin200.04-1.00E+0000.05-9.52E-011.00E+00
TGF-beta receptor200.04-1.00E+0000.05-9.52E-011.00E+00
DNA polymerase processivity factor200.04-1.00E+0000.05-9.52E-011.00E+00
DNA photolyase200.04-1.00E+0000.05-9.52E-011.00E+00
exodeoxyribonuclease100.02-1.00E+0000.02-9.76E-011.00E+00
voltage-gated ion channel100.02-1.00E+0000.02-9.76E-011.00E+00
primase100.02-1.00E+0000.02-9.76E-011.00E+00
phosphatase activator100.02-1.00E+0000.02-9.76E-011.00E+00
reverse transcriptase100.02-1.00E+0000.02-9.76E-011.00E+00

Supplementary Table 4b. Consensus PSD

Proteins from the total PSD exclusive to human or mouse were classified independently using the Panther 'Protein Class' descriptor. Enrichment analysis was done to determine Protein Classes overrepresented in each species set of exclusive molecules. The Benjamini-Hochberg procedure was used to correct for multiple testing. The column 'observed' retrieves the number of proteins identified in each 'Protein Class' while the column 'expected', the number that would have been identified by chance. Over or under-representations are shown by a (+) or (-) symbol respectively. A second sheet contains the same analysis but done only for the molecules from the consensus PSD.

Human and mouse PSD proteins not found in the other specie were classified independenly using the Panther 'Protein Class' descriptor. An enrichment analysis was done to determine Protein Classes overrepresented in each species as compared with the human genome. P-values were corrected for multiple testing using the Benjamini-Hochberg procedure. The colum 'observed' retrives the number of proteins identified in each 'Protein Class' while the column 'expected', the number which would have been identified by chance. Over or underrepresntations are shown by a (+) or (-) symbol respectively.

Protein classes in human PSD as compared with human genome Protein classes in mouse PSD as compared with human genome
PANTHER Protein ClassHomo sapiens genesObservedExpectedover/underCorrected P-valueObservedExpectedover/underP-valueCorrected P-value
cytoskeletal protein441162.35+3.61E-0753.85+3.42E-011.00E+00
actin family cytoskeletal protein222101.18+3.45E-0521.94+5.79E-011.00E+00
oxidoreductase550132.93+5.06E-04104.81+2.36E-023.25E-01
dehydrogenase21081.12+8.88E-0461.84+1.09E-022.10E-01
non-motor actin binding protein11460.61+1.42E-0311+6.32E-011.00E+00
reductase6540.35+1.39E-0230.57+1.99E-022.95E-01
transcription factor2067211-2.18E-02318.06-8.16E-063.94E-04
transferase1512188.05+2.48E-021413.21+4.51E-011.00E+00
microtubule family cytoskeletal protein15650.83+3.32E-0221.36+3.96E-011.00E+00
transfer/carrier protein24861.32+4.27E-0202.17-1.13E-017.40E-01
nucleotide kinase5130.27+4.31E-0220.45+7.40E-026.80E-01
membrane trafficking regulatory protein10740.57+4.31E-0220.94+2.40E-011.00E+00
transaminase2520.13+1.20E-0100.22-8.04E-011.00E+00
dehydratase3120.17+1.63E-0100.27-7.63E-011.00E+00
zinc finger transcription factor80304.27-1.63E-0127.02-2.70E-023.26E-01
lyase10430.55+2.23E-0100.91-4.02E-011.00E+00
kinase67983.61+3.02E-01115.93+3.72E-023.99E-01
membrane traffic protein32151.71+3.02E-0172.81+2.36E-023.25E-01
methyltransferase13030.69+3.02E-0101.14-3.20E-011.00E+00
chaperone13030.69+3.02E-0101.14-3.20E-011.00E+00
non-motor microtubule binding protein5320.28+3.02E-0110.46+3.71E-011.00E+00
actin binding motor protein910.05+4.11E-0100.08-9.24E-011.00E+00
KRAB box transcription factor55202.94-4.26E-0104.82-7.51E-031.61E-01
Unclassified67632836-4.81E-015459.1-2.32E-011.00E+00
Hsp70 family chaperone1310.07+5.12E-0100.11-8.93E-011.00E+00
phosphorylase1310.07+5.12E-0100.11-8.93E-011.00E+00
transmembrane receptor regulatory/adaptor protein8420.45+5.12E-0110.73+5.21E-011.00E+00
storage protein1510.08+5.12E-0100.13-8.77E-011.00E+00
DNA binding protein47602.53-5.12E-0134.16-4.00E-011.00E+00
acyltransferase8820.47+5.18E-0110.77+5.37E-011.00E+00
DNA methyltransferase1710.09+5.39E-0100.15-8.62E-011.00E+00
G-protein20631.1+5.91E-0141.8+1.08E-017.40E-01
cysteine protease inhibitor2110.11+6.20E-0100.18-8.32E-011.00E+00
protease inhibitor10920.58+6.53E-0100.95-3.85E-011.00E+00
protein kinase51052.72+7.55E-0164.46+2.88E-011.00E+00
actin and actin related protein3110.17+7.94E-0110.27+2.37E-011.00E+00
ion channel34101.82-7.94E-01122.98+5.37E-052.07E-03
receptor107635.73-7.94E-01119.4+3.41E-011.00E+00
carbohydrate kinase3510.19+7.94E-0100.31-7.36E-011.00E+00
enzyme modulator85774.56+7.94E-01147.49+1.89E-022.95E-01
heterotrimeric G-protein3610.19+7.94E-0110.31+2.70E-011.00E+00
interleukin superfamily3610.19+7.94E-0100.31-7.30E-011.00E+00
phospholipase3610.19+7.94E-0100.31-7.30E-011.00E+00
metalloprotease14520.77+7.94E-0111.27-6.38E-011.00E+00
apolipoprotein4210.22+8.58E-0100.37-6.93E-011.00E+00
small GTPase15820.84+8.58E-0131.38+1.61E-019.42E-01
HMG box transcription factor4410.23+8.58E-0100.38-6.80E-011.00E+00
microtubule binding motor protein4610.24+8.73E-0100.4-6.69E-011.00E+00
extracellular matrix glycoprotein5510.29+1.00E+0010.48+3.82E-011.00E+00
lipase5710.3+1.00E+0000.5-6.07E-011.00E+00
phosphatase modulator6310.34+1.00E+0000.55-5.76E-011.00E+00
homeobox transcription factor23301.24-1.00E+0002.04-1.29E-018.03E-01
helix-turn-helix transcription factor23301.24-1.00E+0002.04-1.29E-018.03E-01
glycosyltransferase22901.22-1.00E+0022-6.76E-011.00E+00
transporter109845.85-1.00E+00199.6+3.64E-038.78E-02
hydrolase45412.42-1.00E+0013.97-9.14E-026.81E-01
G-protein coupled receptor44712.38-1.00E+0043.91+5.50E-011.00E+00
RNA helicase7110.38+1.00E+0010.62+4.63E-011.00E+00
extracellular matrix protein7210.38+1.00E+0010.63+4.68E-011.00E+00
nucleic acid binding146667.8-1.00E+002812.81+7.88E-052.53E-03
serine protease inhibitor7910.42+1.00E+0000.69-5.01E-011.00E+00
mRNA processing factor17900.95-1.00E+0001.56-2.08E-011.00E+00
cation transporter17800.95-1.00E+0011.56-5.39E-011.00E+00
isomerase9410.5+1.00E+0000.82-4.39E-011.00E+00
signaling molecule96165.12+1.00E+00138.4+7.97E-026.81E-01
amino acid transporter9810.52+1.00E+0000.86-4.24E-011.00E+00
structural protein28021.49+1.00E+0032.45+4.43E-011.00E+00
protein phosphatase11110.59+1.00E+0010.97+6.22E-011.00E+00
protease47632.53+1.00E+0034.16-4.00E-011.00E+00
membrane-bound signaling molecule13300.71-1.00E+0021.16+3.24E-011.00E+00
ubiquitin-protein ligase13210.7+1.00E+0001.15-3.14E-011.00E+00
cysteine protease12100.64-1.00E+0011.06-7.15E-011.00E+00
basic helix-loop-helix transcription factor12000.64-1.00E+0001.05-3.49E-011.00E+00
RNA binding protein72743.87+1.00E+00206.35+6.78E-063.94E-04
serine protease15310.81+1.00E+0001.34-2.61E-011.00E+00
G-protein modulator27811.48-1.00E+0062.43+3.64E-023.99E-01
immunoglobulin receptor superfamily15510.83+1.00E+0011.35-6.07E-011.00E+00
defense/immunity protein10700.57-1.00E+0000.94-3.92E-011.00E+00
acetyltransferase10500.56-1.00E+0010.92+6.01E-011.00E+00
cytokine15910.85+1.00E+0001.39-2.48E-011.00E+00
kinase modulator10300.55-1.00E+0030.9+6.24E-026.02E-01
ligand-gated ion channel10100.54-1.00E+0040.88+1.24E-022.18E-01
growth factor16510.88+1.00E+0001.44-2.35E-011.00E+00
peptide hormone16910.9+1.00E+0021.48+4.35E-011.00E+00
ligase26011.38-1.00E+0012.27-3.35E-011.00E+00
transcription cofactor25511.36-1.00E+0002.23-1.06E-017.40E-01
cell adhesion molecule9300.5-1.00E+0010.81+5.57E-011.00E+00
potassium channel8900.47-1.00E+0020.78+1.83E-011.00E+00
ribosomal protein18410.98+1.00E+00161.61+1.18E-112.28E-09
nucleotidyltransferase8400.45-1.00E+0000.73-4.79E-011.00E+00
phosphatase23011.22-1.00E+0032.01+3.26E-011.00E+00
DNA helicase8000.43-1.00E+0000.7-4.96E-011.00E+00
guanyl-nucleotide exchange factor7900.42-1.00E+0010.69+4.99E-011.00E+00
chromatin/chromatin-binding protein7400.39-1.00E+0010.65+4.77E-011.00E+00
oxygenase7400.39-1.00E+0010.65+4.77E-011.00E+00
ATP-binding cassette (ABC) transporter7400.39-1.00E+0010.65+4.77E-011.00E+00
cytokine receptor21311.13-1.00E+0011.86-4.43E-011.00E+00
cell junction protein6700.36-1.00E+0000.59-5.56E-011.00E+00
calcium-binding protein6300.34-1.00E+0000.55-5.76E-011.00E+00
ribonucleoprotein6100.32-1.00E+0000.53-5.86E-011.00E+00
oxidase5700.3-1.00E+0000.5-6.07E-011.00E+00
translation factor5600.3-1.00E+0020.49+8.68E-026.81E-01
histone5400.29-1.00E+0000.47-6.23E-011.00E+00
ATP synthase5100.27-1.00E+0010.45+3.60E-011.00E+00
chemokine4800.26-1.00E+0000.42-6.57E-011.00E+00
replication origin binding protein4700.25-1.00E+0000.41-6.63E-011.00E+00
carbohydrate transporter4600.24-1.00E+0000.4-6.69E-011.00E+00
nuclear hormone receptor4600.24-1.00E+0000.4-6.69E-011.00E+00
kinase activator4500.24-1.00E+0010.39+3.25E-011.00E+00
damaged DNA-binding protein4500.24-1.00E+0000.39-6.75E-011.00E+00
hydroxylase4400.23-1.00E+0000.38-6.80E-011.00E+00
SNARE protein3700.2-1.00E+0040.32+3.42E-049.43E-03
anion channel3700.2-1.00E+0000.32-7.24E-011.00E+00
nucleotide phosphatase3500.19-1.00E+0010.31+2.64E-011.00E+00
nuclease3500.19-1.00E+0010.31+2.64E-011.00E+00
myelin protein3300.18-1.00E+0010.29+2.51E-011.00E+00
intracellular calcium-sensing protein3300.18-1.00E+0000.29-7.49E-011.00E+00
endoribonuclease3300.18-1.00E+0000.29-7.49E-011.00E+00
immunoglobulin3300.18-1.00E+0000.29-7.49E-011.00E+00
calmodulin3300.18-1.00E+0000.29-7.49E-011.00E+00
calcium channel3100.17-1.00E+0060.27+4.02E-073.88E-05
type I cytokine receptor3100.17-1.00E+0000.27-7.63E-011.00E+00
vesicle coat protein3000.16-1.00E+0010.26+2.31E-011.00E+00
tight junction3000.16-1.00E+0000.26-7.69E-011.00E+00
major histocompatibility complex antigen2800.15-1.00E+0000.24-7.83E-011.00E+00
phosphatase inhibitor2800.15-1.00E+0000.24-7.83E-011.00E+00
neuropeptide2800.15-1.00E+0000.24-7.83E-011.00E+00
phosphodiesterase2700.14-1.00E+0000.24-7.90E-011.00E+00
peroxidase2700.14-1.00E+0000.24-7.90E-011.00E+00
glycosidase2600.14-1.00E+0000.23-7.97E-011.00E+00
immunoglobulin superfamily cell adhesion molecule2500.13-1.00E+0010.22+1.96E-011.00E+00
tubulin2500.13-1.00E+0010.22+1.96E-011.00E+00
esterase2500.13-1.00E+0000.22-8.04E-011.00E+00
exoribonuclease2400.13-1.00E+0000.21-8.11E-011.00E+00
basic leucine zipper transcription factor2400.13-1.00E+0000.21-8.11E-011.00E+00
CREB transcription factor2400.13-1.00E+0000.21-8.11E-011.00E+00
cyclase2300.12-1.00E+0000.2-8.18E-011.00E+00
tumor necrosis factor receptor2200.12-1.00E+0000.19-8.25E-011.00E+00
RNA methyltransferase2200.12-1.00E+0000.19-8.25E-011.00E+00
gap junction2100.11-1.00E+0000.18-8.32E-011.00E+00
adenylate cyclase2100.11-1.00E+0000.18-8.32E-011.00E+00
endodeoxyribonuclease2000.11-1.00E+0000.17-8.40E-011.00E+00
chaperonin2000.11-1.00E+0000.17-8.40E-011.00E+00
aminoacyl-tRNA synthetase2000.11-1.00E+0000.17-8.40E-011.00E+00
sodium channel2000.11-1.00E+0000.17-8.40E-011.00E+00
centromere DNA-binding protein1800.1-1.00E+0000.16-8.54E-011.00E+00
antibacterial response protein1800.1-1.00E+0000.16-8.54E-011.00E+00
mitochondrial carrier protein1700.09-1.00E+0000.15-8.62E-011.00E+00
interferon superfamily1700.09-1.00E+0000.15-8.62E-011.00E+00
decarboxylase1700.09-1.00E+0000.15-8.62E-011.00E+00
galactosidase1600.09-1.00E+0000.14-8.69E-011.00E+00
kinase inhibitor1500.08-1.00E+0000.13-8.77E-011.00E+00
glucosidase1500.08-1.00E+0000.13-8.77E-011.00E+00
surfactant1500.08-1.00E+0000.13-8.77E-011.00E+00
DNA-directed RNA polymerase1500.08-1.00E+0000.13-8.77E-011.00E+00
aspartic protease1400.07-1.00E+0010.12+1.15E-017.40E-01
mutase1400.07-1.00E+0000.12-8.85E-011.00E+00
deaminase1200.06-1.00E+0000.1-9.00E-011.00E+00
DNA glycosylase1200.06-1.00E+0000.1-9.00E-011.00E+00
intermediate filament1100.06-1.00E+0010.1+9.17E-026.81E-01
tumor necrosis factor family member1100.06-1.00E+0000.1-9.08E-011.00E+00
intermediate filament binding protein1000.05-1.00E+0010.09+8.37E-026.81E-01
Hsp90 family chaperone1000.05-1.00E+0000.09-9.16E-011.00E+00
DNA-directed DNA polymerase1000.05-1.00E+0000.09-9.16E-011.00E+00
extracellular matrix structural protein900.05-1.00E+0000.08-9.24E-011.00E+00
carbohydrate phosphatase900.05-1.00E+0000.08-9.24E-011.00E+00
annexin900.05-1.00E+0000.08-9.24E-011.00E+00
protein kinase receptor800.04-1.00E+0000.07-9.32E-011.00E+00
neurotrophic factor800.04-1.00E+0000.07-9.32E-011.00E+00
epimerase/racemase700.04-1.00E+0000.06-9.41E-011.00E+00
viral protein700.04-1.00E+0000.06-9.41E-011.00E+00
viral coat protein700.04-1.00E+0000.06-9.41E-011.00E+00
DNA strand-pairing protein700.04-1.00E+0000.06-9.41E-011.00E+00
DNA ligase600.03-1.00E+0010.05+5.11E-025.19E-01
amylase600.03-1.00E+0000.05-9.49E-011.00E+00
helicase500.03-1.00E+0000.04-9.57E-011.00E+00
amino acid kinase500.03-1.00E+0000.04-9.57E-011.00E+00
pyrophosphatase500.03-1.00E+0000.04-9.57E-011.00E+00
transketolase500.03-1.00E+0000.04-9.57E-011.00E+00
metalloprotease inhibitor400.02-1.00E+0000.03-9.66E-011.00E+00
aldolase400.02-1.00E+0000.03-9.66E-011.00E+00
DNA topoisomerase400.02-1.00E+0000.03-9.66E-011.00E+00
deacetylase200.01-1.00E+0000.02-9.83E-011.00E+00
calsequestrin200.01-1.00E+0000.02-9.83E-011.00E+00
TGF-beta receptor200.01-1.00E+0000.02-9.83E-011.00E+00
DNA polymerase processivity factor200.01-1.00E+0000.02-9.83E-011.00E+00
DNA photolyase200.01-1.00E+0000.02-9.83E-011.00E+00
exodeoxyribonuclease100.01-1.00E+0000.01-9.91E-011.00E+00
voltage-gated ion channel100.01-1.00E+0000.01-9.91E-011.00E+00
primase100.01-1.00E+0000.01-9.91E-011.00E+00
phosphatase activator100.01-1.00E+0000.01-9.91E-011.00E+00
transaldolase100.01-1.00E+0000.01-9.91E-011.00E+00
reverse transcriptase100.01-1.00E+0000.01-9.91E-011.00E+00

Supplementary Table 5. Pathways enriched in human and mouse unique or enriched proteins.

Proteins from the consensus PSD exclusive or significantly enriched in human or mouse were classified independently using the Panther 'Pathway' descriptor. Enrichment analysis was done to determine Pathways overrepresented in each species set of specific proteins. The Benjamini-Hochberg procedure was used to correct for multiple testing. The column 'observed' retrieves the number of proteins identified in each 'Pathway' while the column 'expected', the number that would have been identified by chance. Over or under-representations are shown by a (+) or (-) symbol respectively.

Pathway (Human)Homo sapiens genesObservedExpected(over/under)Corrected P-valuePathway (Mouse)ObservedExpected(over/under)P-valueCorrected P-value
Unclassified17270121148.32-5.47E-06Ionotropic glutamate receptor pathway15.73+2.65E-154.08E-13
Pyrimidine Metabolism154.13+7.70E-04Metabotropic glutamate receptor group III pathway11.95+5.19E-097.99E-07
Parkinson disease977.83+1.25E-03Metabotropic glutamate receptor group II pathway7.64+4.67E-067.19E-04
Axon guidance mediated by semaphorins374.32+1.23E-02Synaptic_vesicle_trafficking6.50+1.41E-052.17E-03
Apoptosis signaling pathway11961.02+1.93E-02Metabotropic glutamate receptor group I pathway5.35+3.34E-055.14E-03
Glycolysis243.21+3.16E-02GABA-B_receptor_II_signaling5.54+2.47E-043.80E-02
De novo purine biosynthesis333.28+6.67E-02Unclassified214235.05-2.69E-044.14E-02
EGF receptor signaling pathway13051.12+1.07E-01Heterotrimeric G-protein signaling pathway-Gq alpha and Go alpha mediated pathway81.82+5.74E-048.84E-02
Integrin signalling pathway19661.68+1.25E-01Thyrotropin-releasing hormone receptor signaling pathway5.84+1.73E-032.66E-01
TCA cycle162.14+1.32E-01Endothelin signaling pathway51.20+7.53E-031.00E+00
Cytoskeletal regulation by Rho GTPase984.84+1.45E-01Heterotrimeric G-protein signaling pathway-Gi alpha and Gs alpha mediated pathway72.23+7.75E-031.00E+00
5-Hydroxytryptamine degredation192.16+1.45E-01Muscarinic acetylcholine receptor 2 and 4 signaling pathway4.84+1.07E-021.00E+00
Toll receptor signaling pathway563.48+1.45E-01Beta2 adrenergic receptor signaling pathway3.60+2.29E-021.00E+00
Huntington disease16151.38+1.45E-01Beta1 adrenergic receptor signaling pathway3.60+2.29E-021.00E+00
Ubiquitin proteasome pathway693.59+2.07E-01Alpha adrenergic receptor signaling pathway2.31+3.98E-021.00E+00
VEGF signaling pathway693.59+2.07E-01Endogenous_cannabinoid_signaling2.33+4.29E-021.00E+00
FGF signaling pathway12441.06+2.07E-01Nicotinic acetylcholine receptor signaling pathway41.31+4.33E-021.00E+00
Phenylalanine biosynthesis31.03+2.17E-01Cytoskeletal regulation by Rho GTPase41.33+4.61E-021.00E+00
Tyrosine biosynthesis41.03+2.74E-01Beta3 adrenergic receptor signaling pathway2.35+4.95E-021.00E+00
Synaptic_vesicle_trafficking372.32+3.08E-01Muscarinic acetylcholine receptor 1 and 3 signaling pathway3.83+5.16E-021.00E+00
Serine glycine biosynthesis51.04+3.08E-01Proline biosynthesis1.05+5.30E-021.00E+00
Asparagine and aspartate biosynthesis51.04+3.08E-01Hedgehog signaling pathway2.38+5.64E-021.00E+00
Angiogenesis17641.51+4.26E-01Cortocotropin releasing factor receptor signaling pathway2.41+6.37E-021.00E+00
Pentose phosphate pathway81.07+4.26E-015HT4 type receptor mediated signaling pathway2.42+6.74E-021.00E+00
Arginine biosynthesis81.07+4.26E-01Huntington disease52.19+7.08E-021.00E+00
Phenylethylamine degradation101.09+4.87E-01Adrenaline and noradrenaline biosynthesis2.44+7.12E-021.00E+00
Inflammation mediated by chemokine and cytokine signaling pathway27252.34+4.94E-01EGF receptor signaling pathway41.77+1.03E-011.00E+00
Ras Pathway752.64+7.48E-01Integrin signalling pathway52.67+1.31E-011.00E+00
Dopamine receptor mediated signaling pathway802.69+8.02E-01Notch signaling pathway2.64+1.35E-011.00E+00
T cell activation882.76+8.98E-01Transcription regulation by bZIP transcription factor2.73+1.68E-011.00E+00
Interferon-gamma signaling pathway291.25+1.00E+00TCA cycle1.22+1.96E-011.00E+00
Wnt signaling pathway31812.73-1.00E+00Oxytocin receptor mediated signaling pathway2.82+1.97E-011.00E+00
Insulin/IGF pathway-mitogen activated protein kinase kinase/MAP kinase cascade341.29+1.00E+005HT3 type receptor mediated signaling pathway1.24+2.17E-011.00E+00
FAS signaling pathway361.31+1.00E+00VEGF signaling pathway2.94+2.42E-011.00E+00
Alzheimer disease-presenilin pathway12221.05+1.00E+005HT2 type receptor mediated signaling pathway2.94+2.42E-011.00E+00
Angiotensin II-stimulated signaling through G proteins and beta-arrestin401.34+1.00E+00Ras Pathway21.02+2.72E-011.00E+00
Heterotrimeric G-protein signaling pathway-Gq alpha and Go alpha mediated pathway13401.15-1.00E+00Histamine H2 receptor mediated signaling pathway1.34+2.89E-011.00E+00
p38 MAPK pathway461.40+1.00E+00Axon guidance mediated by Slit/Robo1.34+2.89E-011.00E+00
PDGF signaling pathway14821.27+1.00E+00Dopamine receptor mediated signaling pathway21.09+2.97E-011.00E+00
TGF-beta signaling pathway14921.28+1.00E+00Insulin/IGF pathway-protein kinase B signaling cascade01.20-3.01E-011.00E+00
Alzheimer disease-amyloid secretase pathway671.58+1.00E+00Inflammation mediated by chemokine and cytokine signaling pathway53.70+3.13E-011.00E+00
B cell activation731.63+1.00E+00Cadherin signaling pathway31.99+3.20E-011.00E+00
Insulin/IGF pathway-protein kinase B signaling cascade880.76-1.00E+00TGF-beta signaling pathway32.03+3.31E-011.00E+00
Endothelin signaling pathway881.76+1.00E+00Opioid prodynorphin pathway1.42+3.44E-011.00E+00
Metabotropic glutamate receptor group III pathway700.60-1.00E+00Opioid proenkephalin pathway1.42+3.44E-011.00E+00
5HT2 type receptor mediated signaling pathway690.59-1.00E+00Opioid proopiomelanocortin pathway1.44+3.53E-011.00E+00
Nicotinic acetylcholine receptor signaling pathway961.82+1.00E+00Interleukin signaling pathway12.16-3.62E-011.00E+00
Thyrotropin-releasing hormone receptor signaling pathway620.53-1.00E+00Wnt signaling pathway34.33-3.70E-011.00E+00
Muscarinic acetylcholine receptor 2 and 4 signaling pathway620.53-1.00E+00Axon guidance mediated by netrin1.48+3.79E-011.00E+00
Heterotrimeric G-protein signaling pathway-Gi alpha and Gs alpha mediated pathway16411.41-1.00E+00Parkinson disease21.32+3.81E-011.00E+00
Muscarinic acetylcholine receptor 1 and 3 signaling pathway610.52-1.00E+00Ubiquitin proteasome pathway0.94-3.90E-011.00E+00
Oxytocin receptor mediated signaling pathway600.52-1.00E+00PDGF signaling pathway12.01-4.01E-011.00E+00
Interleukin signaling pathway15911.37-1.00E+00Alzheimer disease-amyloid secretase pathway0.91-4.01E-011.00E+00
Oxidative stress response560.48-1.00E+00Heterotrimeric G-protein signaling pathway-rod outer segment phototransduction1.53+4.12E-011.00E+00
p53 pathway1141.98+1.00E+005HT1 type receptor mediated signaling pathway1.60+4.51E-011.00E+00
Transcription regulation by bZIP transcription factor540.46-1.00E+00Toll receptor signaling pathway0.76-4.66E-011.00E+00
Ionotropic glutamate receptor pathway540.46-1.00E+00Oxidative stress response0.76-4.66E-011.00E+00
p53 pathway feedback loops 2520.45-1.00E+00PI3 kinase pathway21.59+4.73E-011.00E+00
Cadherin signaling pathway14611.25-1.00E+00FGF signaling pathway21.69+5.04E-011.00E+00
Blood coagulation480.41-1.00E+00Alzheimer disease-presenilin pathway11.66-5.05E-011.00E+00
Notch signaling pathway470.40-1.00E+00p53 pathway feedback loops 21.71+5.08E-011.00E+00
Metabotropic glutamate receptor group II pathway470.40-1.00E+00Apoptosis signaling pathway11.62-5.18E-011.00E+00
Histamine H1 receptor mediated signaling pathway470.40-1.00E+00Blood coagulation0.65-5.20E-011.00E+00
Beta2 adrenergic receptor signaling pathway440.38-1.00E+00Histamine H1 receptor mediated signaling pathway0.64-5.27E-011.00E+00
Beta1 adrenergic receptor signaling pathway440.38-1.00E+00p38 MAPK pathway0.63-5.34E-011.00E+00
5HT1 type receptor mediated signaling pathway440.38-1.00E+00p53 pathway11.55-5.40E-011.00E+00
GABA-B_receptor_II_signaling400.34-1.00E+00Angiogenesis22.40-5.70E-011.00E+00
Heterotrimeric G-protein signaling pathway-rod outer segment phototransduction390.33-1.00E+00Angiotensin II-stimulated signaling through G proteins and beta-arrestin0.54-5.80E-011.00E+00
General transcription regulation370.32-1.00E+00Axon guidance mediated by semaphorins0.50-6.04E-011.00E+00
PI3 kinase pathway11711.00-1.00E+00General transcription regulation0.50-6.04E-011.00E+00
Axon guidance mediated by netrin350.30-1.00E+00FAS signaling pathway0.49-6.12E-011.00E+00
Enkephalin release330.28-1.00E+00Insulin/IGF pathway-mitogen activated protein kinase kinase/MAP kinase cascade0.46-6.29E-011.00E+00
Adrenaline and noradrenaline biosynthesis320.27-1.00E+00B cell activation1.99+6.30E-011.00E+00
Opioid proopiomelanocortin pathway320.27-1.00E+00De novo purine biosynthesis0.45-6.38E-011.00E+00
Hypoxia response via HIF activation320.27-1.00E+00Enkephalin release0.45-6.38E-011.00E+00
Opioid prodynorphin pathway310.27-1.00E+00Hypoxia response via HIF activation0.44-6.47E-011.00E+00
Opioid proenkephalin pathway310.27-1.00E+00T cell activation11.20-6.63E-011.00E+00
5HT4 type receptor mediated signaling pathway310.27-1.00E+00Interferon-gamma signaling pathway0.39-6.74E-011.00E+00
Cortocotropin releasing factor receptor signaling pathway300.26-1.00E+00Nicotine degradation0.34-7.11E-011.00E+00
Hedgehog signaling pathway280.24-1.00E+00p53 pathway by glucose deprivation0.34-7.11E-011.00E+00
Metabotropic glutamate receptor group I pathway260.22-1.00E+00Glycolysis0.33-7.21E-011.00E+00
Beta3 adrenergic receptor signaling pathway260.22-1.00E+00Cell cycle0.30-7.41E-011.00E+00
Nicotine degradation250.21-1.00E+00DNA replication0.29-7.51E-011.00E+00
p53 pathway by glucose deprivation250.21-1.00E+00General transcription by RNA polymerase I0.27-7.62E-011.00E+00
Histamine H2 receptor mediated signaling pathway250.21-1.00E+005-Hydroxytryptamine degredation0.26-7.72E-011.00E+00
Axon guidance mediated by Slit/Robo250.21-1.00E+00Androgen/estrogene/progesterone biosynthesis0.26-7.72E-011.00E+00
Endogenous_cannabinoid_signaling240.21-1.00E+00De novo pyrmidine ribonucleotides biosythesis0.24-7.83E-011.00E+00
Alpha adrenergic receptor signaling pathway230.20-1.00E+00Plasminogen activating cascade0.24-7.83E-011.00E+00
Cell cycle220.19-1.00E+00De novo pyrimidine deoxyribonucleotide biosynthesis0.24-7.83E-011.00E+00
DNA replication210.18-1.00E+00JAK/STAT signaling pathway0.23-7.93E-011.00E+00
General transcription by RNA polymerase I200.17-1.00E+00Pyrimidine Metabolism0.20-8.15E-011.00E+00
Androgen/estrogene/progesterone biosynthesis190.16-1.00E+00Salvage pyrimidine ribonucleotides0.19-8.26E-011.00E+00
De novo pyrmidine ribonucleotides biosythesis180.15-1.00E+00Pyruvate metabolism0.19-8.26E-011.00E+00
Plasminogen activating cascade180.15-1.00E+00Heme biosynthesis0.18-8.38E-011.00E+00
De novo pyrimidine deoxyribonucleotide biosynthesis180.15-1.00E+00Cholesterol biosynthesis0.18-8.38E-011.00E+00
5HT3 type receptor mediated signaling pathway180.15-1.00E+00Fructose galactose metabolism0.16-8.49E-011.00E+00
JAK/STAT signaling pathway170.15-1.00E+00Vitamin D metabolism and pathway0.16-8.49E-011.00E+00
Salvage pyrimidine ribonucleotides140.12-1.00E+00Vasopressin synthesis0.16-8.49E-011.00E+00
Pyruvate metabolism140.12-1.00E+00Circadian clock system0.16-8.49E-011.00E+00
Heme biosynthesis130.11-1.00E+00Phenylethylamine degradation0.14-8.73E-011.00E+00
Cholesterol biosynthesis130.11-1.00E+00Formyltetrahydroformate biosynthesis0.14-8.73E-011.00E+00
Fructose galactose metabolism120.10-1.00E+00mRNA splicing0.12-8.85E-011.00E+00
Vitamin D metabolism and pathway120.10-1.00E+00Pentose phosphate pathway0.11-8.97E-011.00E+00
Vasopressin synthesis120.10-1.00E+00Arginine biosynthesis0.11-8.97E-011.00E+00
Circadian clock system120.10-1.00E+00Adenine and hypoxanthine salvage pathway0.11-8.97E-011.00E+00
Formyltetrahydroformate biosynthesis100.09-1.00E+00ATP synthesis0.11-8.97E-011.00E+00
mRNA splicing90.08-1.00E+002-arachidonoylglycerol biosynthesis0.10-9.09E-011.00E+00
Adenine and hypoxanthine salvage pathway80.07-1.00E+00N-acetylglucosamine metabolism0.10-9.09E-011.00E+00
ATP synthesis80.07-1.00E+00Mannose metabolism0.10-9.09E-011.00E+00
2-arachidonoylglycerol biosynthesis70.06-1.00E+00P53 pathway feedback loops 10.10-9.09E-011.00E+00
N-acetylglucosamine metabolism70.06-1.00E+00Purine metabolism0.08-9.22E-011.00E+00
Mannose metabolism70.06-1.00E+00Folate biosynthesis0.08-9.22E-011.00E+00
P53 pathway feedback loops 170.06-1.00E+00Coenzyme A biosynthesis0.08-9.22E-011.00E+00
Purine metabolism60.05-1.00E+00Gamma-aminobutyric acid synthesis0.08-9.22E-011.00E+00
Folate biosynthesis60.05-1.00E+005-Hydroxytryptamine biosynthesis0.08-9.22E-011.00E+00
Coenzyme A biosynthesis60.05-1.00E+00Serine glycine biosynthesis0.07-9.34E-011.00E+00
Gamma-aminobutyric acid synthesis60.05-1.00E+00Asparagine and aspartate biosynthesis0.07-9.34E-011.00E+00
5-Hydroxytryptamine biosynthesis60.05-1.00E+00Tyrosine biosynthesis0.05-9.47E-011.00E+00
Xanthine and guanine salvage pathway40.03-1.00E+00Xanthine and guanine salvage pathway0.05-9.47E-011.00E+00
Salvage pyrimidine deoxyribonucleotides40.03-1.00E+00Salvage pyrimidine deoxyribonucleotides0.05-9.47E-011.00E+00
Proline biosynthesis40.03-1.00E+00O-antigen biosynthesis0.05-9.47E-011.00E+00
O-antigen biosynthesis40.03-1.00E+00Methylmalonyl pathway0.05-9.47E-011.00E+00
Methylmalonyl pathway40.03-1.00E+00Methylcitrate cycle0.05-9.47E-011.00E+00
Methylcitrate cycle40.03-1.00E+00Glutamine glutamate conversion0.05-9.47E-011.00E+00
Glutamine glutamate conversion40.03-1.00E+00Ascorbate degradation0.05-9.47E-011.00E+00
Ascorbate degradation40.03-1.00E+00Phenylalanine biosynthesis0.04-9.60E-011.00E+00
Vitamin B6 metabolism30.03-1.00E+00Vitamin B6 metabolism0.04-9.60E-011.00E+00
Valine biosynthesis30.03-1.00E+00Valine biosynthesis0.04-9.60E-011.00E+00
S adenosyl methionine biosynthesis30.03-1.00E+00S adenosyl methionine biosynthesis0.04-9.60E-011.00E+00
Ornithine degradation30.03-1.00E+00Ornithine degradation0.04-9.60E-011.00E+00
Isoleucine biosynthesis30.03-1.00E+00Isoleucine biosynthesis0.04-9.60E-011.00E+00
Acetate utilization30.03-1.00E+00Acetate utilization0.04-9.60E-011.00E+00
Threonine biosynthesis20.02-1.00E+00Threonine biosynthesis0.03-9.73E-011.00E+00
Thiamine metabolism20.02-1.00E+00Thiamine metabolism0.03-9.73E-011.00E+00
Sulfate assimilation20.02-1.00E+00Sulfate assimilation0.03-9.73E-011.00E+00
Succinate to proprionate conversion20.02-1.00E+00Succinate to proprionate conversion0.03-9.73E-011.00E+00
Pyridoxal phosphate salvage pathway20.02-1.00E+00Pyridoxal phosphate salvage pathway0.03-9.73E-011.00E+00
PLP biosynthesis20.02-1.00E+00PLP biosynthesis0.03-9.73E-011.00E+00
Lysine biosynthesis20.02-1.00E+00Lysine biosynthesis0.03-9.73E-011.00E+00
Lipoate_biosynthesis20.02-1.00E+00Lipoate_biosynthesis0.03-9.73E-011.00E+00
Leucine biosynthesis20.02-1.00E+00Leucine biosynthesis0.03-9.73E-011.00E+00
Carnitine metabolism20.02-1.00E+00Carnitine metabolism0.03-9.73E-011.00E+00
Carnitine and CoA metabolism20.02-1.00E+00Carnitine and CoA metabolism0.03-9.73E-011.00E+00
Histamine synthesis20.02-1.00E+00Histamine synthesis0.03-9.73E-011.00E+00
Aminobutyrate degradation20.02-1.00E+00Aminobutyrate degradation0.03-9.73E-011.00E+00
Alanine biosynthesis20.02-1.00E+00Alanine biosynthesis0.03-9.73E-011.00E+00
Triacylglycerol metabolism10.01-1.00E+00Triacylglycerol metabolism0.01-9.86E-011.00E+00
Bupropion_degradation10.01-1.00E+00Bupropion_degradation0.01-9.86E-011.00E+00
Anandamide_degradation10.01-1.00E+00Anandamide_degradation0.01-9.86E-011.00E+00
Methionine biosynthesis10.01-1.00E+00Methionine biosynthesis0.01-9.86E-011.00E+00
Flavin biosynthesis10.01-1.00E+00Flavin biosynthesis0.01-9.86E-011.00E+00
Cysteine biosynthesis10.01-1.00E+00Cysteine biosynthesis0.01-9.86E-011.00E+00
Cobalamin biosynthesis10.01-1.00E+00Cobalamin biosynthesis0.01-9.86E-011.00E+00
Allantoin degradation10.01-1.00E+00Allantoin degradation0.01-9.86E-011.00E+00
1.00E+001.00E+00

Supplementary Table 6. GO Biological Process term enrichment in human and mouse unique or enriched proteins.

Proteins from the consensus PSD exclusive or significantly enriched in human or mouse were classified independently using the Gene Ontology (GO) term 'Biological Process'. Enrichment analysis was done to determine Biological Processes overrepresented in each species set of specific proteins. The Benjamini-Hochberg procedure was used to correct for multiple testing. The column 'observed' retrieves the number of proteins identified in each 'Biological Process' while the column 'expected', the number that would have been identified by chance. Over or under-representations are shown by a (+) or (-) symbol respectively.

Biological ProcessHomo sapiens genesObservedExpected(over/under)Corrected P-valueBiological ProcessObservedExpected(over/under)P-valueCorrected P-value
Unclassified71082561.05-1.36E-07neurological system process4915.72+1.62E-122.93E-10
protein folding197141.69+2.61E-07synaptic transmission306.29+2.75E-122.93E-10
transcription1993117.12-1.48E-05system process5219.19+5.21E-113.70E-09
transcription from RNA polymerase II promoter1987117.06-1.48E-05cell communication9449.42+9.05E-114.82E-09
protein transport12543010.77+1.48E-05nerve-nerve synaptic transmission131.14+2.49E-101.06E-08
intracellular protein transport12543010.77+1.48E-05"nucleobase, nucleoside, nucleotide and nucleic acid metabolic process"1244.87-6.11E-102.17E-08
regulation of transcription from RNA polymerase II promoter1563013.42-2.58E-05cellular process11872.49+1.96E-095.96E-08
cellular component morphogenesis734196.3+4.64E-04regulation of transcription from RNA polymerase II promoter121.27-5.76E-091.53E-07
anatomical structure morphogenesis734196.3+4.64E-04transport6432.24+5.90E-081.40E-06
response to stress265112.28+4.64E-04cell-cell signaling3211.73+3.53E-077.52E-06
protein metabolic process28034424.07+8.04E-04transcription627.13-4.73E-079.02E-06
vesicle-mediated transport801196.88+1.20E-03transcription from RNA polymerase II promoter627.04-5.08E-079.02E-06
cellular component organization989208.49+5.82E-03signal transduction8046.97+5.55E-079.09E-06
protein complex assembly7350.63+6.59E-03vesicle-mediated transport2910.9+2.12E-063.23E-05
transport23693620.35+6.59E-03protein transport3617.07+2.12E-053.01E-04
metabolic process75118564.51+1.24E-02intracellular protein transport3617.07+2.12E-053.01E-04
intracellular signaling cascade1017198.73+1.59E-02neurotransmitter secretion133.17+2.40E-053.01E-04
"nucleobase, nucleoside, nucleotide and nucleic acid metabolic process"32971528.32-2.90E-02exocytosis143.77+3.42E-054.05E-04
cellular process53266345.74+2.90E-02translation164.82+3.61E-054.05E-04
glycolysis7240.62+3.88E-02protein amino acid phosphorylation228.96+1.19E-041.27E-03
cell motion448103.85+5.76E-02neuronal action potential propagation50.65+5.62E-045.63E-03
primary metabolic process71317761.24+7.86E-02response to stimulus415.18-5.86E-045.63E-03
monosaccharide metabolic process15151.3+9.45E-02immune system process922.82-6.08E-045.63E-03
endocytosis35383.03+9.99E-02Unclassified7296.74-8.54E-047.58E-03
generation of precursor metabolites and energy28572.45+9.99E-02synaptic vesicle exocytosis81.99+9.93E-048.46E-03
pyrimidine base metabolic process5530.47+9.99E-02ion transport198.55+1.13E-039.26E-03
G-protein coupled receptor protein signaling pathway68015.84-1.45E-01ferredoxin metabolic process20.08+3.15E-032.49E-02
synaptic transmission46293.97+1.45E-01cation transport156.89+4.40E-033.35E-02
system development1206410.36-1.48E-01DNA metabolic process05.08-5.95E-034.37E-02
tricarboxylic acid cycle2620.22+1.48E-01intracellular signaling cascade2413.84+6.72E-034.77E-02
cell-cell adhesion44203.8-1.48E-01primary metabolic process7897.06-8.59E-035.80E-02
neuromuscular synaptic transmission2720.23+1.53E-01RNA metabolic process16.72-8.72E-035.80E-02
cell surface receptor linked signal transduction1628713.98-1.74E-01immune response16.47-1.10E-027.10E-02
fatty acid metabolic process20451.75+2.02E-01dorsal/ventral axis specification30.5+1.46E-029.15E-02
reproduction36803.16-2.51E-01cell adhesion2011.76+1.55E-029.43E-02
protein modification process11771610.11+2.79E-01metabolic process85102.23-1.71E-021.01E-01
tRNA aminoacylation for protein translation4220.36+2.90E-01proteolysis613.43-1.79E-021.03E-01
neurotransmitter secretion23352+2.90E-01protein metabolic process5138.15+1.83E-021.03E-01
gamete generation33502.88-2.97E-01protein modification process2516.02+1.92E-021.05E-01
purine base metabolic process10030.86+2.97E-01muscle contraction94.1+2.34E-021.22E-01
response to stimulus1115159.58+2.98E-01cell surface receptor linked signal transduction3222.16+2.35E-021.22E-01
protein amino acid phosphorylation658105.65+2.98E-01G-protein coupled receptor protein signaling pathway169.26+2.52E-021.28E-01
system process14101812.11+2.98E-01anion transport41.22+3.56E-021.76E-01
pentose-phosphate shunt810.07+3.21E-01asymmetric protein localization20.3+3.67E-021.78E-01
RNA metabolic process49414.24-3.40E-01protein localization20.3+3.67E-021.78E-01
carbohydrate metabolic process687105.9+3.40E-01phosphate metabolic process51.91+4.39E-022.03E-01
mRNA processing29802.56-3.40E-01protein targeting51.96+4.85E-022.20E-01
respiratory electron transport chain26252.25+3.40E-01tricarboxylic acid cycle20.35+4.95E-022.20E-01
cellular amino acid metabolic process26652.28+3.50E-01"nuclear mRNA splicing, via spliceosome"02.97-5.06E-022.20E-01
cellular amino acid and derivative metabolic process26652.28+3.50E-01cytokinesis41.39+5.20E-022.22E-01
ion transport62825.39-3.76E-01calcium-mediated signaling52.15+6.65E-022.78E-01
exocytosis27752.38+3.76E-01DNA repair02.61-7.24E-022.97E-01
cellular defense response26402.27-4.07E-01nitric oxide biosynthetic process10.08+7.84E-023.15E-01
receptor-mediated endocytosis13131.13+4.07E-01nitric oxide mediated signal transduction10.08+7.84E-023.15E-01
cytokine-mediated signaling pathway26102.24-4.07E-01mRNA processing14.06-8.60E-023.33E-01
mesoderm development75436.48-4.15E-01mitosis95.31+8.80E-023.35E-01
nervous system development73836.34-4.44E-01macrophage activation02.29-1.01E-013.77E-01
muscle contraction30152.59+4.44E-01mesoderm development610.26-1.10E-014.04E-01
neurological system process1155149.92+4.44E-01DNA replication02.11-1.20E-014.16E-01
developmental process20932317.98+4.61E-01reproduction25.01-1.22E-014.16E-01
cell adhesion86447.42-4.61E-01response to stress13.61-1.23E-014.16E-01
oxidative phosphorylation7620.65+4.78E-01cellular defense response13.59-1.25E-014.16E-01
"nuclear mRNA splicing, via spliceosome"21801.87-5.14E-01general transcription from RNA polymerase II promoter20.61+1.26E-014.16E-01
pattern specification process20701.78-5.51E-01monosaccharide metabolic process02.06-1.27E-014.16E-01
DNA metabolic process37313.2-5.51E-01cytokine-mediated signaling pathway13.55-1.29E-014.16E-01
coenzyme metabolic process9220.79+5.95E-01organelle organization13.55-1.29E-014.16E-01
cation transport50624.35-5.95E-01segment specification02.03-1.31E-014.16E-01
translation35453.04+5.95E-01oxygen and reactive oxygen species metabolic process20.69+1.54E-014.82E-01
immune system process16771814.4+5.99E-01transmembrane receptor protein tyrosine kinase signaling pathway13.29-1.58E-014.88E-01
spermatogenesis18701.61-6.06E-01gamete generation24.56-1.65E-014.98E-01
nuclear transport9820.84+6.18E-01MAPKKK cascade63.7+1.69E-014.98E-01
skeletal system development18101.55-6.21E-01establishment or maintenance of chromatin architecture13.2-1.70E-014.98E-01
cytokinesis10220.88+6.39E-01carbohydrate metabolic process69.35-1.72E-014.98E-01
angiogenesis17201.48-6.53E-01"nucleobase, nucleoside, nucleotide and nucleic acid transport"20.75+1.73E-014.98E-01
mitosis39053.35+6.90E-01localization20.76+1.78E-015.06E-01
cell communication36313531.18+6.90E-01B cell mediated immunity01.7-1.81E-015.07E-01
RNA localization3410.29+6.90E-01lipid transport42.26+1.92E-015.31E-01
fatty acid biosynthetic process3410.29+6.90E-01generation of precursor metabolites and energy63.88+1.95E-015.33E-01
blood coagulation15801.36-6.90E-01carbohydrate transport20.87+2.17E-015.84E-01
response to external stimulus15801.36-6.90E-01nitrogen compound metabolic process10.24+2.17E-015.84E-01
DNA replication15501.33-6.92E-01cellular amino acid catabolic process20.88+2.22E-015.84E-01
embryonic development15101.3-7.07E-01phospholipid metabolic process12.8-2.29E-015.95E-01
segment specification14901.28-7.11E-01fatty acid metabolic process12.78-2.34E-015.96E-01
ectoderm development82757.1-7.15E-01extracellular transport01.42-2.42E-015.96E-01
cell cycle1152129.89+7.19E-01protein amino acid glycosylation12.72-2.43E-015.96E-01
lipid metabolic process83697.18+7.23E-01natural killer cell activation01.4-2.45E-015.96E-01
cell-cell signaling86297.4+7.91E-01induction of apoptosis53.36+2.48E-015.96E-01
B cell mediated immunity12501.07-8.21E-01protein folding12.68-2.51E-015.96E-01
organelle organization26112.24-8.21E-01steroid metabolic process12.68-2.51E-015.96E-01
protein targeting14421.24+8.31E-01hemopoiesis01.37-2.52E-015.96E-01
synaptic vesicle exocytosis14621.25+8.36E-01purine base metabolic process01.36-2.56E-015.99E-01
induction of apoptosis24712.12-8.40E-01nuclear transport01.33-2.63E-016.09E-01
"nucleobase, nucleoside, nucleotide and nucleic acid transport"5510.47+8.40E-01spermatogenesis12.55-2.77E-016.30E-01
localization5610.48+8.40E-01sulfur metabolic process01.28-2.77E-016.30E-01
tRNA metabolic process5610.48+8.40E-01visual perception53.54+2.81E-016.30E-01
transmembrane receptor protein tyrosine kinase signaling pathway24212.08-8.40E-01coenzyme metabolic process01.25-2.85E-016.32E-01
visual perception26032.23+8.40E-01response to interferon-gamma01.24-2.89E-016.35E-01
establishment or maintenance of chromatin architecture23512.02-8.40E-01muscle organ development12.45-2.96E-016.37E-01
heart development10500.9-8.40E-01JAK-STAT cascade01.21-2.97E-016.37E-01
extracellular transport10400.89-8.40E-01cellular component morphogenesis129.99+3.00E-016.37E-01
natural killer cell activation10300.88-8.40E-01anatomical structure morphogenesis129.99+3.00E-016.37E-01
immune response47534.08-8.40E-01homeostatic process01.18-3.05E-016.37E-01
lipid transport16621.43+8.40E-01neuromuscular synaptic transmission10.37+3.08E-016.37E-01
hemopoiesis10100.87-8.40E-01transcription initiation from RNA polymerase II promoter01.16-3.14E-016.43E-01
signal transduction34513129.64+8.40E-01cell-matrix adhesion01.14-3.18E-016.43E-01
polysaccharide metabolic process22511.93-8.40E-01response to toxin01.13-3.22E-016.43E-01
cellular amino acid biosynthetic process6410.55+8.40E-01system development1416.41-3.23E-016.43E-01
cellular amino acid catabolic process6510.56+8.40E-01meiosis21.21+3.42E-016.75E-01
JNK cascade9800.84-8.40E-01endocytosis64.8+3.49E-016.75E-01
blood circulation9600.82-8.45E-01DNA recombination01.05-3.50E-016.75E-01
anion transport9000.77-8.45E-01rRNA metabolic process01.05-3.50E-016.75E-01
JAK-STAT cascade8900.76-8.45E-01oxidative phosphorylation01.03-3.55E-016.75E-01
complement activation7310.63+8.45E-01blood coagulation12.15-3.66E-016.79E-01
apoptosis68155.85-8.45E-01response to external stimulus12.15-3.66E-016.79E-01
phospholipid metabolic process20611.77-8.45E-01negative regulation of apoptosis12.14-3.69E-016.79E-01
homeostatic process8700.75-8.45E-01protein complex assembly00.99-3.70E-016.79E-01
proteolysis98798.48+8.45E-01glycolysis00.98-3.75E-016.83E-01
transcription initiation from RNA polymerase II promoter8500.73-8.45E-01antigen processing and presentation00.98-3.75E-016.83E-01
DNA recombination7710.66+8.45E-01embryonic development12.06-3.90E-016.98E-01
I-kappaB kinase/NF-kappaB cascade8400.72-8.45E-01RNA catabolic process00.93-3.96E-017.03E-01
nerve-nerve synaptic transmission8400.72-8.45E-01fertilization00.93-3.96E-017.03E-01
protein amino acid glycosylation20011.72-8.45E-01polysaccharide metabolic process23.06-4.08E-017.07E-01
steroid metabolic process19711.69-8.45E-01cell motion76.1+4.10E-017.07E-01
vitamin transport7900.68-8.45E-01lipid metabolic process1011.38-4.12E-017.07E-01
anterior/posterior axis specification7900.68-8.45E-01angiogenesis32.34+4.15E-017.07E-01
DNA repair19211.65-8.45E-01apoptosis89.27-4.18E-017.07E-01
response to toxin8310.71+8.45E-01nervous system development1110.04+4.23E-017.09E-01
cell-matrix adhesion8410.72+8.45E-01skeletal system development32.46+4.47E-017.44E-01
rRNA metabolic process7700.66-8.45E-01tRNA metabolic process00.76-4.66E-017.69E-01
glycogen metabolic process8510.73+8.45E-01pyrimidine base metabolic process00.75-4.73E-017.75E-01
female gamete generation7600.65-8.45E-01respiratory electron transport chain43.57+4.78E-017.75E-01
meiosis8910.76+8.57E-01amino acid transport10.65+4.80E-017.75E-01
antigen processing and presentation7200.62-8.57E-01chromosome segregation11.74-4.80E-017.75E-01
muscle organ development18011.55-8.57E-01cellular amino acid metabolic process43.62+4.90E-017.78E-01
response to interferon-gamma9110.78+8.57E-01cellular amino acid and derivative metabolic process43.62+4.90E-017.78E-01
cholesterol metabolic process9310.8+8.60E-01cell cycle1515.68-4.97E-017.78E-01
sulfur metabolic process9410.81+8.60E-01developmental process2828.49-5.11E-017.92E-01
RNA catabolic process6800.58-8.60E-01regulation of biological process00.67-5.13E-017.92E-01
fertilization6800.58-8.60E-01regulation of vasoconstriction00.67-5.13E-017.92E-01
macrophage activation16811.44-8.70E-01cellular component organization1313.46-5.21E-017.93E-01
carbohydrate transport6400.55-8.70E-01receptor-mediated endocytosis21.78+5.33E-017.98E-01
sensory perception38433.3-8.70E-01cyclic nucleotide metabolic process00.63-5.34E-017.98E-01
MAPKKK cascade27222.34-8.73E-01pattern specification process32.82+5.36E-017.98E-01
calcium-mediated signaling15811.36-8.95E-01cellular calcium ion homeostasis00.61-5.42E-018.00E-01
negative regulation of apoptosis15711.35-8.95E-01ectoderm development1111.26-5.48E-018.00E-01
oxygen and reactive oxygen species metabolic process5100.44-9.36E-01vitamin metabolic process00.6-5.49E-018.00E-01
regulation of biological process4900.42-9.36E-01transmembrane receptor protein serine/threonine kinase signaling pathway00.6-5.49E-018.00E-01
regulation of vasoconstriction4900.42-9.36E-01RNA elongation from RNA polymerase II promoter00.59-5.57E-018.00E-01
phosphate metabolic process14011.2-9.36E-01defense response to bacterium00.59-5.57E-018.00E-01
neuronal action potential propagation4800.41-9.36E-01tRNA aminoacylation for protein translation00.57-5.64E-018.00E-01
amino acid transport4800.41-9.36E-01phagocytosis00.56-5.72E-018.00E-01
cyclic nucleotide metabolic process4600.4-9.36E-01sensory perception55.23-5.76E-018.00E-01
general transcription from RNA polymerase II promoter4500.39-9.36E-01sensory perception of sound00.54-5.80E-018.00E-01
cellular calcium ion homeostasis4500.39-9.36E-01heart development11.43-5.81E-018.00E-01
vitamin metabolic process4400.38-9.36E-01cellular amino acid biosynthetic process10.87+5.82E-018.00E-01
transmembrane receptor protein serine/threonine kinase signaling pathway4400.38-9.36E-01mRNA 3'-end processing00.53-5.88E-018.03E-01
RNA elongation from RNA polymerase II promoter4300.37-9.36E-01cell-cell adhesion66.02-6.04E-018.18E-01
defense response to bacterium4300.37-9.36E-01sensory perception of pain00.5-6.04E-018.18E-01
chromosome segregation12811.1-9.36E-01JNK cascade11.33-6.15E-018.18E-01
phagocytosis4100.35-9.36E-01antigen processing and presentation of peptide or polysaccharide antigen via MHC class II00.48-6.21E-018.18E-01
sensory perception of sound4000.34-9.38E-01blood circulation11.31-6.24E-018.18E-01
mRNA 3'-end processing3900.33-9.40E-01RNA localization00.46-6.29E-018.18E-01
sensory perception of pain3700.32-9.51E-01fatty acid biosynthetic process00.46-6.29E-018.18E-01
dorsal/ventral axis specification3700.32-9.51E-01complement activation10.99+6.30E-018.18E-01
antigen processing and presentation of peptide or polysaccharide antigen via MHC class II3500.3-9.55E-01cellular glucose homeostasis00.45-6.38E-018.20E-01
cellular glucose homeostasis3300.28-9.66E-01cholesterol metabolic process11.27-6.39E-018.20E-01
mRNA polyadenylation3200.27-9.69E-01mRNA polyadenylation00.44-6.47E-018.25E-01
gluconeogenesis3000.26-9.79E-01gluconeogenesis00.41-6.65E-018.43E-01
mRNA transcription2900.25-9.79E-01mRNA transcription00.39-6.74E-018.45E-01
mammary gland development2900.25-9.79E-01mammary gland development00.39-6.74E-018.45E-01
endoderm development2800.24-9.79E-01glycogen metabolic process11.16-6.78E-018.45E-01
protein amino acid acetylation2700.23-9.82E-01I-kappaB kinase/NF-kappaB cascade11.14-6.83E-018.46E-01
mitochondrion organization2600.22-9.82E-01endoderm development00.38-6.83E-018.46E-01
mitochondrial transport2600.22-9.82E-01protein amino acid acetylation00.37-6.92E-018.46E-01
fatty acid beta-oxidation2500.21-9.82E-01mitochondrion organization00.35-7.02E-018.46E-01
acyl-CoA metabolic process2400.21-9.85E-01mitochondrial transport00.35-7.02E-018.46E-01
porphyrin metabolic process2200.19-9.88E-01vitamin transport11.08-7.08E-018.46E-01
asymmetric protein localization2200.19-9.88E-01anterior/posterior axis specification11.08-7.08E-018.46E-01
protein localization2200.19-9.88E-01fatty acid beta-oxidation00.34-7.11E-018.46E-01
vitamin biosynthetic process2100.18-9.88E-01acyl-CoA metabolic process00.33-7.21E-018.51E-01
protein amino acid lipidation2100.18-9.88E-01female gamete generation11.03-7.23E-018.51E-01
termination of RNA polymerase II transcription1900.16-9.93E-01porphyrin metabolic process00.3-7.41E-018.67E-01
lysosomal transport1800.15-9.93E-01vitamin biosynthetic process00.29-7.51E-018.74E-01
nitrogen compound metabolic process1800.15-9.93E-01protein amino acid lipidation00.29-7.51E-018.74E-01
sex determination1700.15-9.93E-01termination of RNA polymerase II transcription00.26-7.72E-018.89E-01
regulation of carbohydrate metabolic process1700.15-9.93E-01lysosomal transport00.24-7.83E-018.97E-01
phosphate transport1600.14-9.93E-01sex determination00.23-7.93E-019.03E-01
gut mesoderm development1500.13-9.95E-01regulation of carbohydrate metabolic process00.23-7.93E-019.03E-01
peroxisomal transport1400.12-9.95E-01phosphate transport00.22-8.04E-019.06E-01
"regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process"1400.12-9.95E-01gut mesoderm development00.2-8.15E-019.14E-01
sensory perception of chemical stimulus1200.1-9.95E-01peroxisomal transport00.19-8.26E-019.21E-01
protein amino acid methylation1000.09-9.95E-01"regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process"00.19-8.26E-019.21E-01
protein amino acid ADP-ribosylation1000.09-9.95E-01sensory perception of chemical stimulus00.16-8.49E-019.37E-01
DNA catabolic process1000.09-9.95E-01protein amino acid methylation00.14-8.73E-019.52E-01
sensory perception of taste1000.09-9.95E-01protein amino acid ADP-ribosylation00.14-8.73E-019.52E-01
regulation of liquid surface tension900.08-9.95E-01DNA catabolic process00.14-8.73E-019.52E-01
response to pheromone700.06-9.95E-01sensory perception of taste00.14-8.73E-019.52E-01
pinocytosis700.06-9.95E-01regulation of liquid surface tension00.12-8.85E-019.52E-01
"transcription, RNA-dependent"600.05-9.95E-01pentose-phosphate shunt00.11-8.97E-019.60E-01
nitric oxide biosynthetic process600.05-9.95E-01response to pheromone00.1-9.09E-019.68E-01
regulation of amino acid metabolic process600.05-9.95E-01pinocytosis00.1-9.09E-019.68E-01
ferredoxin metabolic process600.05-9.95E-01"transcription, RNA-dependent"00.08-9.22E-019.70E-01
unsaturated fatty acid biosynthetic process600.05-9.95E-01regulation of amino acid metabolic process00.08-9.22E-019.70E-01
nitric oxide mediated signal transduction600.05-9.95E-01unsaturated fatty acid biosynthetic process00.08-9.22E-019.70E-01
disaccharide metabolic process500.04-9.95E-01disaccharide metabolic process00.07-9.34E-019.70E-01
polyphosphate catabolic process400.03-9.99E-01polyphosphate catabolic process00.05-9.47E-019.79E-01
mRNA capping300.03-1.00E+00mRNA capping00.04-9.60E-019.88E-01
regulation of phosphate metabolic process300.03-1.00E+00regulation of phosphate metabolic process00.04-9.60E-019.88E-01
sensory perception of smell200.02-1.00E+00sensory perception of smell00.03-9.73E-019.92E-01
nitrogen utilization200.02-1.00E+00nitrogen utilization00.03-9.73E-019.92E-01
vitamin catabolic process100.01-1.00E+00vitamin catabolic process00.01-9.86E-019.95E-01
catabolic process100.01-1.00E+00catabolic process00.01-9.86E-019.95E-01
bile acid metabolic process100.01-1.00E+00bile acid metabolic process00.01-9.86E-019.95E-01
11.00E+00

Supplementary Table 7. Proteins related to axon guidance or cell morphology.

Proteins shown are either members of the group of molecules involved in 'axon guidance mediated by semaphorins', as defined by Panther, or are known to be involved in this process (literature), or belong to the Biological Process: "cellular component morphogenesis'. Of all molecules belonging to the later group only those that are unique or significantly enriched in human PSD were considered.

Gene Name HGNC ID MGI ID Panther Pathway: Axon guidance mediated by Semaphorins Panther Biological Process Cellular Compoenet Morphogenesis Involved in Axonguidance mediated by sempahorins acording to Literature Abundance Fold Difference (AFD) Mouse/Human Significantly Enriched
CRMP1HGNC:2365MGI:107793YESYES0.141Human
DPYSL2HGNC:3014MGI:1349763YESYES0.122Human
DPYSL3HGNC:3015MGI:1349762YESYES0.032Human
CDK5HGNC:1774MGI:101765YESYES0.733NOT
PLXNA1HGNC:9099MGI:107685YESYES0.302NOT
RAC1HGNC:9801MGI:97845YESYES1.736NOT
RHOAHGNC:667MGI:1096342YESYES1.071NOT
PAK1HGNC:8590MGI:1339975YESYES0.154Human
ARHGEF2HGNC:682MGI:103264YES1.331NOT
FYNHGNC:4037MGI:95602YES0.813NOT
RHOBHGNC:668MGI:107949YES2.387NOT
ROCK2HGNC:10252MGI:107926YES1.988NOT
PLXNA2HGNC:9100MGI:107684YESHuman Only
PLXNA3HGNC:9101MGI:107683YESHuman Only
CDC42HGNC:1736MGI:106211YES1.530NOT
GSK3BHGNC:4617MGI:1861437YES0.936NOT
PLXNA4HGNC:9102MGI:2179061YES0.484NOT
CFL1HGNC:1874MGI:101757YES0.134Human
DNM1LHGNC:2973MGI:1921256YES0.246Human
GFAPHGNC:4235MGI:95697YES0.028Human
MAPRE2HGNC:6891MGI:106271YES0.047Human
MSNHGNC:7373MGI:97167YES0.038Human
PLP1HGNC:9086MGI:97623YES0.073Human
VIMHGNC:12692MGI:98932YES0.021Human
TUBB2CHGNC:20771MGI:1915472YES0.484Human
TPPPHGNC:24164MGI:1920198YES0.201Human
MAP4HGNC:6862MGI:97178YES0.167Human
DYNC1LI2HGNC:2966MGI:1077380.262Human
CAPGHGNC:1474MGI:1098259YESHuman Only
KIF21AHGNC:19349MGI:109188YESHuman Only
TBCBHGNC:1989MGI:1913661YESHuman Only
VCLHGNC:12665MGI:98927YESHuman Only
TLN1HGNC:11845MGI:1099832YESHuman Only
FLNAHGNC:3754MGI:95556YESHuman Only

Supplementary Table 8. Functional comparison of all PSD proteins identified in human and mouse.

All human and mouse PSD proteins were classified together using the Panther 'Protein Class' descriptor. An enrichment analysis was done to determine Protein Classes overrepresented compared with the human genome. The Benjamini-Hochberg procedure was used to correct for multiple testing. The column 'observed' retrieves the number of proteins identified in each 'Protein Class' while the column 'expected', the number that would have been identified by chance. Over or under-representations are shown by a (+) or (-) symbol respectively.

PANTHER Protein Class Homo sapiens genes Observed Expected Over/Under P-value Corrected P-value
Cytoskeletal protein44116341.91+2.0E-473.9E-45
Transcription factor206741196.41-1.9E-441.9E-42
Membrane traffic protein32112330.5+2.3E-371.5E-35
Actin family cytoskeletal protein2229621.1+2.6E-331.3E-31
Zinc finger transcription factor803776.3-6.5E-252.1E-23
Enzyme modulator85718381.43+1.7E-234.6E-22
G-protein2066819.57+6.5E-181.1E-16
G-protein modulator2787926.42+5.7E-179.2E-16
Oxidoreductase55012152.26+9.4E-171.4E-15
Chaperone1305012.35+5.0E-166.9E-15
Transporter1098193104.34+5.9E-167.6E-15
Microtubule family cytoskeletal protein1565514.82+6.4E-167.8E-15
Kinase67913764.52+7.1E-168.0E-15
Cation transporter1785716.91+1.1E-141.1E-13
Unclassified6763508642.64-1.6E-111.4E-10
RNA binding protein72712969.08+3.0E-112.5E-10
Transferase1512215143.67+3.9E-093.0E-08
Helix-turn-helix transcription factor233322.14-4.6E-072.8E-06
Ion channel3415832.4+2.7E-051.4E-04
DNA binding protein4762545.23-6.7E-042.8E-03
Intermediate filament1161.05+7.4E-043.0E-03
Nucleic acid binding1466173139.3+2.3E-038.7E-03
Hydrolase4546343.14+2.4E-038.9E-03
Cytokine159515.11-2.5E-039.2E-03
Peptide hormone169616.06-3.8E-031.3E-02
Signaling molecule9616891.32-5.6E-031.9E-02
Lyase104199.88+6.3E-032.1E-02
Protease inhibitor109310.36-7.8E-032.5E-02
Protease4763045.23-9.9E-033.1E-02
Extracellular matrix protein72146.84+1.1E-023.2E-02
Ligase2603724.71+1.2E-023.6E-02
Structural protein2803726.61+3.2E-028.2E-02
Receptor107685102.24-4.1E-021.0E-01
Defense/immunity protein107510.17-6.1E-021.4E-01
Phosphatase2302921.86+8.1E-021.7E-01
Growth factor1651015.68-8.8E-021.8E-01
Isomerase94138.93+1.2E-012.3E-01
Calcium-binding protein6395.99+1.5E-012.7E-01
Intracellular calcium-sensing protein3353.14+2.1E-013.4E-01
Transfer/carrier protein2482623.57+3.3E-014.8E-01
Cell adhesion molecule9378.84-3.4E-014.8E-01
Cytokine receptor2131820.24-3.6E-014.9E-01
Cyclase2332.19+3.7E-015.0E-01
Lipase5765.42+4.6E-015.6E-01
Viral protein700.67-5.1E-015.8E-01
Kinase modulator103109.79+5.2E-015.8E-01
Cell junction protein6766.37-5.5E-016.1E-01
Phosphatase modulator6365.99+5.5E-016.1E-01
Non-motor actin binding protein1146110.83+3.2E-261.2E-24
KRAB box transcription factor552152.45-4.4E-221.0E-20
Ribosomal protein1847017.48+1.3E-212.8E-20
Dehydrogenase2106919.95+4.7E-189.0E-17
Membrane trafficking regulatory protein1074410.17+2.9E-153.1E-14
ATP synthase51284.85+4.2E-134.0E-12
Small GTPase1585015.01+6.8E-136.2E-12
Nucleotide kinase51234.85+2.0E-091.6E-08
Non-motor microtubule binding protein53225.04+1.9E-081.4E-07
Protein kinase5109148.46+2.0E-081.4E-07
Guanyl-nucleotide exchange factor79277.51+2.7E-081.9E-07
SNARE protein37183.52+3.6E-082.4E-07
Heterotrimeric G-protein36173.42+1.3E-078.4E-07
Vesicle coat protein30152.85+3.5E-072.1E-06
Homeobox transcription factor233322.14-4.6E-072.8E-06
Hsp70 family chaperone13101.24+7.3E-074.2E-06
Chaperonin20121.9+7.9E-074.4E-06
Transmembrane receptor regulatory/adaptor protein84257.98+1.1E-065.6E-06
Tubulin25112.38+3.9E-052.0E-04
Microtubule binding motor protein46154.37+5.2E-052.6E-04
Calcium channel31122.95+5.9E-052.8E-04
Ligand-gated ion channel101239.6+1.6E-047.4E-04
Aminoacyl-tRNA synthetase2091.9+1.6E-047.4E-04
Reductase65176.18+2.4E-041.1E-03
Transcription cofactor255924.23-3.4E-041.5E-03
Intermediate filament binding protein1060.95+4.5E-041.9E-03
Basic helix-loop-helix transcription factor120211.4-8.4E-043.4E-03
Mitochondrial carrier protein1771.62+1.4E-035.5E-03
Carbohydrate kinase35103.33+2.3E-038.7E-03
Peroxidase2782.57+4.9E-031.7E-02
Myelin protein3393.14+5.0E-031.7E-02
Amino acid transporter98189.31+7.3E-032.4E-02
Extracellular matrix glycoprotein55125.23+7.5E-032.4E-02
Amino acid kinase530.48+1.3E-023.7E-02
Acetyltransferase105189.98+1.4E-024.0E-02
Phosphodiesterase2772.57+1.6E-024.6E-02
Hsp90 family chaperone1040.95+1.6E-024.6E-02
Serine protease inhibitor7927.51-2.0E-025.6E-02
RNA helicase71136.75+2.1E-025.7E-02
Anion channel3783.52+2.7E-027.4E-02
Deaminase1241.14+2.9E-027.7E-02
Actin and actin related protein3172.95+3.1E-028.1E-02
Membrane-bound signaling molecule133612.64-3.2E-028.2E-02
G-protein coupled receptor4473142.48-3.9E-021.0E-01
Endoribonuclease3303.14-4.3E-021.1E-01
Serine protease153814.54-4.7E-021.1E-01
Oxidase57105.42+4.9E-021.2E-01
Actin binding motor protein930.86+5.6E-021.3E-01
Aldolase420.38+5.6E-021.3E-01
Storage protein1541.43+5.7E-021.3E-01
Nuclear hormone receptor4614.37-6.8E-021.5E-01
Neuropeptide2802.66-7.0E-021.6E-01
Damaged DNA-binding protein4514.28-7.3E-021.6E-01
Methyltransferase130712.35-7.5E-021.6E-01
HMG box transcription factor4414.18-7.9E-021.7E-01
Oxygenase7437.03-8.0E-021.7E-01
Transketolase520.48+8.3E-021.7E-01
Glycosidase2602.47-8.4E-021.8E-01
Transaldolase110.1+9.1E-021.8E-01
Translation factor5695.32+9.1E-021.8E-01
Immunoglobulin superfamily cell adhesion molecule2552.38+9.3E-021.8E-01
Basic leucine zipper transcription factor2402.28-1.0E-012.0E-01
CREB transcription factor2402.28-1.0E-012.0E-01
Nucleotide phosphatase3563.33+1.2E-012.3E-01
Tumor necrosis factor receptor2202.09-1.2E-012.3E-01
RNA methyltransferase2202.09-1.2E-012.3E-01
DNA helicase8047.6-1.2E-012.3E-01
Interleukin superfamily3613.42-1.4E-012.6E-01
Endodeoxyribonuclease2001.9-1.5E-012.7E-01
Chemokine4824.56-1.7E-013.0E-01
ATP-binding cassette (ABC) transporter7447.03-1.7E-013.0E-01
Immunoglobulin3313.14-1.8E-013.1E-01
Centromere DNA-binding protein1801.71-1.8E-013.1E-01
Metalloprotease1451013.78-1.9E-013.3E-01
Interferon superfamily1701.62-2.0E-013.4E-01
Kinase activator4524.28-2.0E-013.4E-01
Type I cytokine receptor3112.95-2.1E-013.4E-01
Calmodulin3353.14+2.1E-013.4E-01
Extracellular matrix structural protein920.86+2.1E-013.4E-01
Annexin920.86+2.1E-013.4E-01
Hydroxylase4424.18-2.1E-013.4E-01
Transaminase2542.38+2.2E-013.4E-01
Galactosidase1601.52-2.2E-013.4E-01
Potassium channel89118.46+2.3E-013.6E-01
Apolipoprotein4223.99-2.4E-013.7E-01
Kinase inhibitor1501.43-2.4E-013.7E-01
Surfactant1501.43-2.4E-013.7E-01
DNA-directed RNA polymerase1501.43-2.4E-013.7E-01
Major histocompatibility complex antigen2812.66-2.6E-013.9E-01
Phospholipase3653.42+2.6E-013.9E-01
Immunoglobulin receptor superfamily1551714.73+3.1E-014.6E-01
DNA glycosylase1201.14-3.2E-014.7E-01
Adenylate cyclase2132+3.2E-014.7E-01
Glycosyltransferase2291921.76-3.2E-014.7E-01
Exoribonuclease2412.28-3.4E-014.8E-01
Dehydratase3142.95+3.4E-014.8E-01
Phosphorylase1321.24+3.5E-014.9E-01
Tumor necrosis factor family member1101.05-3.5E-014.9E-01
Ribonucleoprotein6175.8+3.6E-014.9E-01
Protein phosphatase1111210.55+3.7E-015.0E-01
Aspartic protease1421.33+3.8E-015.1E-01
Mutase1421.33+3.8E-015.1E-01
DNA-directed DNA polymerase1000.95-3.9E-015.1E-01
Cysteine protease1211011.5-4.0E-015.3E-01
Nucleotidyltransferase8497.98+4.1E-015.3E-01
Cysteine protease inhibitor2112-4.1E-015.3E-01
Gap junction2112-4.1E-015.3E-01
Esterase2532.38+4.2E-015.4E-01
Carbohydrate phosphatase900.86-4.3E-015.4E-01
Amylase610.57+4.4E-015.4E-01
DNA ligase610.57+4.4E-015.4E-01
mRNA processing factor1791817.01+4.4E-015.4E-01
Carbohydrate transporter4654.37+4.4E-015.5E-01
Tight junction3022.85-4.6E-015.6E-01
Protein kinase receptor800.76-4.7E-015.7E-01
Neurotrophic factor800.76-4.7E-015.7E-01
Decarboxylase1721.62+4.8E-015.8E-01
DNA methyltransferase1721.62+4.8E-015.8E-01
Ubiquitin-protein ligase1321312.54+4.9E-015.8E-01
Phosphatase inhibitor2822.66-5.0E-015.8E-01
Antibacterial response protein1821.71+5.1E-015.8E-01
Epimerase/racemase700.67-5.1E-015.8E-01
Viral coat protein700.67-5.1E-015.8E-01
DNA strand-pairing protein700.67-5.1E-015.8E-01
Replication origin binding protein4744.47-5.4E-016.1E-01
Acyltransferase8888.36-5.4E-016.1E-01
Sodium channel2021.9+5.7E-016.3E-01
Nuclease3533.33-5.8E-016.3E-01
Glucosidase1511.43-5.8E-016.4E-01
Histone5455.13-5.9E-016.4E-01
Chromatin/chromatin-binding protein7477.03-5.9E-016.4E-01
Helicase500.48-6.2E-016.7E-01
Pyrophosphatase500.48-6.2E-016.7E-01
Metalloprotease inhibitor400.38-6.8E-017.3E-01
DNA topoisomerase400.38-6.8E-017.3E-01
Deacetylase200.19-8.3E-018.7E-01
Calsequestrin200.19-8.3E-018.7E-01
TGF-beta receptor200.19-8.3E-018.7E-01
DNA polymerase processivity factor200.19-8.3E-018.7E-01
DNA photolyase200.19-8.3E-018.7E-01
Exodeoxyribonuclease100.1-9.1E-019.3E-01
Voltage-gated ion channel100.1-9.1E-019.3E-01
Primase100.1-9.1E-019.3E-01
Phosphatase activator100.1-9.1E-019.3E-01
Reverse transcriptase100.1-9.1E-019.3E-01

Supplementary Table 9a. Pathway analysis of all PSD proteins identified in human and mouse.

All human and mouse PSD proteins were classified together using the Panther 'Pathway' descriptor. An enrichment analysis was done to determine Pathways overrepresented compared with the human genome. The Benjamini-Hochberg procedure was used to correct for multiple testing. The column 'observed' retrieves the number of proteins identified in each 'Pathway' while the column 'expected', the number that would have been identified by chance. Over or under-representations are shown by a (+) or (-) symbol respectively.

Human and mouse PSD proteins were classified using the Panther 'Pathway' descriptor. An enrichment analysis was done to determine Pathways overrepresented as compared with the human genome, a set of mouse brain expressed proteins and a set of genes highly expressed inhuman neurons. P-values were corrected for multiple testing using the Benjamini-Hochberg procedure. The colum 'observed' retrives the number of proteins identified in each 'Pathway' while the column 'expected', the number which would have been identified by chance. Over or underrepresntations are shown by a (+) or (-) symbol respectively.

PSD vs Human Genome
PathwayObservedExpectedover/underP-valueCorrected P-value
Metabotropic glutamate receptor group III pathway446.94+3.09E-214.51E-19
Metabotropic glutamate receptor group II pathway344.85+4.99E-183.64E-16
Muscarinic acetylcholine receptor 1 and 3 signaling pathway355.8+1.44E-167.01E-15
Huntington disease5815.87+2.00E-167.30E-15
Ionotropic glutamate receptor pathway325.13+1.18E-153.43E-14
Thyrotropin-releasing hormone receptor signaling pathway345.89+1.41E-153.43E-14
Synaptic_vesicle_trafficking273.61+2.81E-155.86E-14
Parkinson disease429.5+6.06E-151.11E-13
Heterotrimeric G-protein signaling pathway-Gq alpha and Go alpha mediated pathway4812.73+2.52E-144.09E-13
Oxytocin receptor mediated signaling pathway315.7+1.14E-131.66E-12
5HT2 type receptor mediated signaling pathway336.56+1.51E-132.00E-12
Muscarinic acetylcholine receptor 2 and 4 signaling pathway305.89+1.41E-121.72E-11
Histamine H1 receptor mediated signaling pathway264.47+2.39E-122.68E-11
Beta2 adrenergic receptor signaling pathway254.18+3.57E-123.72E-11
Beta1 adrenergic receptor signaling pathway254.18+3.57E-123.72E-11
Inflammation mediated by chemokine and cytokine signaling pathway6926.89+5.42E-124.95E-11
Cortocotropin releasing factor receptor signaling pathway202.85+3.20E-112.75E-10
Heterotrimeric G-protein signaling pathway-Gi alpha and Gs alpha mediated pathway4815.77+4.02E-113.26E-10
Cytoskeletal regulation by Rho GTPase359.31+8.18E-116.29E-10
5HT1 type receptor mediated signaling pathway234.18+1.27E-109.27E-10
5HT4 type receptor mediated signaling pathway192.95+3.90E-102.71E-09
GABA-B_receptor_II_signaling213.8+7.37E-104.89E-09
Beta3 adrenergic receptor signaling pathway172.47+1.24E-097.87E-09
EGF receptor signaling pathway3912.83+2.66E-091.62E-08
Metabotropic glutamate receptor group I pathway193.42+4.28E-092.50E-08
Unclassified15601647.41-5.90E-093.31E-08
Alpha adrenergic receptor signaling pathway173.04+2.50E-081.35E-07
Histamine H2 receptor mediated signaling pathway152.38+3.47E-081.81E-07
Nicotinic acetylcholine receptor signaling pathway309.22+4.11E-082.07E-07
Endogenous_cannabinoid_signaling142.28+1.37E-076.67E-07
Glycolysis142.38+2.23E-071.05E-06
Axon guidance mediated by semaphorins184.09+3.20E-071.46E-06
Endothelin signaling pathway278.65+4.20E-071.86E-06
Heterotrimeric G-protein signaling pathway-rod outer segment phototransduction174.28+2.62E-061.13E-05
FGF signaling pathway3011.78+5.78E-062.41E-05
TCA cycle101.62+7.62E-063.09E-05
Integrin signalling pathway3817.2+9.08E-063.58E-05
T cell activation269.69+9.80E-063.77E-05
Wnt signaling pathway5630.12+1.33E-054.98E-05
PI3 kinase pathway2710.93+2.74E-051.00E-04
B cell activation217.79+6.27E-052.23E-04
Ras Pathway207.51+1.08E-043.75E-04
Cadherin signaling pathway3013.97+1.22E-044.14E-04
De novo purine biosynthesis123.23+1.38E-044.58E-04
Hedgehog signaling pathway102.38+1.83E-045.94E-04
Adrenaline and noradrenaline biosynthesis113.04+3.22E-041.02E-03
5-Hydroxytryptamine degredation81.9+7.88E-042.45E-03
Apoptosis signaling pathway2411.69+1.01E-033.07E-03
Angiogenesis3318.15+1.03E-033.07E-03
ATP synthesis50.76+1.13E-033.30E-03
5HT3 type receptor mediated signaling pathway71.71+1.93E-035.53E-03
VEGF signaling pathway167.13+2.80E-037.86E-03
Pyrimidine Metabolism61.43+3.47E-039.46E-03
PDGF signaling pathway2715.11+3.50E-039.46E-03
Ubiquitin proteasome pathway156.65+3.58E-039.50E-03
Glutamine glutamate conversion30.38+6.89E-031.80E-02
Pentose phosphate pathway40.76+7.62E-031.95E-02
Axon guidance mediated by Slit/Robo61.9+1.32E-023.32E-02
Phenylethylamine degradation40.95+1.61E-023.98E-02
Adenine and hypoxanthine salvage pathway40.95+1.61E-023.98E-02
Alzheimer disease-amyloid secretase pathway136.75+2.07E-024.95E-02
De novo pyrmidine ribonucleotides biosythesis51.71+3.02E-027.11E-02
General transcription regulation03.42-3.26E-027.55E-02
Phenylalanine biosynthesis20.29+3.37E-027.69E-02
Arginine biosynthesis30.76+4.18E-029.39E-02
Pyruvate metabolism41.33+4.61E-021.02E-01
Circadian clock system30.86+5.56E-021.21E-01
Tyrosine biosynthesis20.38+5.63E-021.21E-01
Proline biosynthesis20.38+5.63E-021.21E-01
FAS signaling pathway73.42+5.92E-021.23E-01
Insulin/IGF pathway-protein kinase B signaling cascade48.46-7.58E-021.55E-01
Oxidative stress response25.7-7.64E-021.55E-01
Serine glycine biosynthesis20.48+8.27E-021.65E-01
Asparagine and aspartate biosynthesis20.48+8.27E-021.65E-01
Triacylglycerol metabolism10.1+9.07E-021.77E-01
Anandamide_degradation10.1+9.07E-021.77E-01
Fructose galactose metabolism31.14+1.08E-012.05E-01
Gamma-aminobutyric acid synthesis20.57+1.12E-012.10E-01
Heme biosynthesis31.24+1.28E-012.37E-01
General transcription by RNA polymerase I01.9-1.49E-012.72E-01
Axon guidance mediated by netrin52.85+1.60E-012.88E-01
Interleukin signaling pathway1115.3-1.65E-012.92E-01
Blood coagulation24.56-1.66E-012.92E-01
Sulfate assimilation10.19+1.73E-012.97E-01
Pyridoxal phosphate salvage pathway10.19+1.73E-012.97E-01
Aminobutyrate degradation10.19+1.73E-012.97E-01
Purine metabolism20.76+1.77E-012.97E-01
Hypoxia response via HIF activation13.04-1.93E-013.20E-01
Toll receptor signaling pathway85.89+2.41E-013.95E-01
Vitamin B6 metabolism10.29+2.48E-014.02E-01
De novo pyrimidine deoxyribonucleotide biosynthesis31.81+2.71E-014.35E-01
Alzheimer disease-presenilin pathway1411.59+2.76E-014.36E-01
TGF-beta signaling pathway1113.78-2.78E-014.36E-01
Formyltetrahydroformate biosynthesis21.05+2.81E-014.36E-01
Androgen/estrogene/progesterone biosynthesis31.9+2.96E-014.53E-01
Interferon-gamma signaling pathway42.76+2.98E-014.53E-01
p53 pathway by glucose deprivation12.38-3.14E-014.71E-01
Methylmalonyl pathway10.38+3.16E-014.71E-01
Ascorbate degradation10.38+3.16E-014.71E-01
Cell cycle32.09+3.48E-015.06E-01
Cholesterol biosynthesis21.24+3.50E-015.06E-01
p53 pathway feedback loops 264.94+3.74E-015.35E-01
Salvage pyrimidine ribonucleotides21.33+3.84E-015.44E-01
p53 pathway1210.74+3.89E-015.46E-01
DNA replication12-4.07E-015.66E-01
mRNA splicing00.86-4.25E-015.77E-01
Insulin/IGF pathway-mitogen activated protein kinase kinase/MAP kinase cascade43.33+4.25E-015.77E-01
JAK/STAT signaling pathway11.9-4.33E-015.77E-01
Transcription regulation by bZIP transcription factor45.04-4.34E-015.77E-01
Xanthine and guanine salvage pathway10.57+4.35E-015.77E-01
Coenzyme A biosynthesis10.57+4.35E-015.77E-01
2-arachidonoylglycerol biosynthesis10.67+4.86E-016.34E-01
Plasminogen activating cascade21.71+5.10E-016.58E-01
N-acetylglucosamine metabolism00.67-5.14E-016.58E-01
Mannose metabolism00.67-5.14E-016.58E-01
P53 pathway feedback loops 100.67-5.14E-016.58E-01
Notch signaling pathway44.47-5.38E-016.71E-01
Folate biosynthesis00.57-5.65E-016.99E-01
5-Hydroxytryptamine biosynthesis00.57-5.65E-016.99E-01
Vitamin D metabolism and pathway11.33-6.16E-017.49E-01
Salvage pyrimidine deoxyribonucleotides00.38-6.84E-018.25E-01
O-antigen biosynthesis00.38-6.84E-018.25E-01
Methylcitrate cycle00.38-6.84E-018.25E-01
Vasopressin synthesis11.14-6.84E-018.25E-01
Valine biosynthesis00.29-7.52E-018.78E-01
S adenosyl methionine biosynthesis00.29-7.52E-018.78E-01
Ornithine degradation00.29-7.52E-018.78E-01
Isoleucine biosynthesis00.29-7.52E-018.78E-01
Acetate utilization00.29-7.52E-018.78E-01
Threonine biosynthesis00.19-8.27E-019.29E-01
Thiamine metabolism00.19-8.27E-019.29E-01
Succinate to proprionate conversion00.19-8.27E-019.29E-01
PLP biosynthesis00.19-8.27E-019.29E-01
Lysine biosynthesis00.19-8.27E-019.29E-01
Lipoate_biosynthesis00.19-8.27E-019.29E-01
Leucine biosynthesis00.19-8.27E-019.29E-01
Carnitine metabolism00.19-8.27E-019.29E-01
Carnitine and CoA metabolism00.19-8.27E-019.29E-01
Histamine synthesis00.19-8.27E-019.29E-01
Alanine biosynthesis00.19-8.27E-019.29E-01
Bupropion_degradation00.1-9.09E-019.41E-01
Methionine biosynthesis00.1-9.09E-019.41E-01
Flavin biosynthesis00.1-9.09E-019.41E-01
Cysteine biosynthesis00.1-9.09E-019.41E-01
Cobalamin biosynthesis00.1-9.09E-019.41E-01
Allantoin degradation00.1-9.09E-019.41E-01

Supplementary Table 9b. Pathway analysis summary of all PSD proteins identified in human and mouse.

All human and mouse PSD proteins were classified together using the Panther 'Pathway' descriptor. An enrichment analysis was done to determine Pathways overrepresented compared with the human genome. The Benjamini-Hochberg procedure was used to correct for multiple testing. The column 'observed' retrieves the number of proteins identified in each 'Pathway' while the column 'expected', the number that would have been identified by chance. Over or under-representations are shown by a (+) or (-) symbol respectively.

Human and mouse PSD proteins were classified using the Panther 'Pathway' descriptor. An enrichment analysis was done to determine Pathways overrepresented as compared with the human genome, a set of mouse brain expressed proteins and a set of genes highly expressed inhuman neurons. P-values were corrected for multiple testing using the Benjamini-Hochberg procedure. The colum 'observed' retrives the number of proteins identified in each 'Pathway' while the column 'expected', the number which would have been identified by chance. Over or underrepresntations are shown by a (+) or (-) symbol respectively.

PathwayCorrected P-value vs GenomeCorrected P-value vs Mouse BrainCorrected P-value vs NeuronSignificantly overreprresented against the 3 neural lists
Metabotropic glutamate receptor group III pathway4.51E-192.13E-062.41E-03YES
Metabotropic glutamate receptor group II pathway3.64E-163.51E-054.34E-04YES
Muscarinic acetylcholine receptor 1 and 3 signaling pathway7.01E-152.10E-051.93E-06YES
Huntington disease7.30E-154.35E-049.66E-07YES
Ionotropic glutamate receptor pathway3.43E-146.33E-064.24E-03YES
Thyrotropin-releasing hormone receptor signaling pathway3.43E-142.10E-054.34E-04YES
Synaptic_vesicle_trafficking5.86E-141.42E-041.21E-02YES
Parkinson disease1.11E-138.85E-031.04E-07YES
Heterotrimeric G-protein signaling pathway-Gq alpha and Go alpha mediated pathway4.09E-133.25E-059.10E-06YES
Oxytocin receptor mediated signaling pathway1.66E-128.75E-052.99E-03YES
5HT2 type receptor mediated signaling pathway2.00E-127.41E-055.96E-03YES
Muscarinic acetylcholine receptor 2 and 4 signaling pathway1.72E-112.87E-033.52E-05YES
Histamine H1 receptor mediated signaling pathway2.68E-117.41E-059.04E-04YES
Beta2 adrenergic receptor signaling pathway3.72E-111.55E-033.21E-02YES
Beta1 adrenergic receptor signaling pathway3.72E-111.55E-033.21E-02YES
Inflammation mediated by chemokine and cytokine signaling pathway4.95E-112.12E-055.95E-07YES
Cortocotropin releasing factor receptor signaling pathway2.75E-101.33E-022.40E-04YES
Heterotrimeric G-protein signaling pathway-Gi alpha and Gs alpha mediated pathway3.26E-102.87E-039.79E-05YES
Cytoskeletal regulation by Rho GTPase6.29E-101.75E-041.96E-03YES
5HT1 type receptor mediated signaling pathway9.27E-105.24E-037.43E-03YES
5HT4 type receptor mediated signaling pathway2.71E-091.56E-023.07E-03YES
EGF receptor signaling pathway1.62E-082.23E-024.34E-04YES
Metabotropic glutamate receptor group I pathway2.50E-083.54E-053.00E-02YES
Histamine H2 receptor mediated signaling pathway1.81E-072.86E-024.97E-02YES
Nicotinic acetylcholine receptor signaling pathway2.07E-073.79E-043.52E-05YES
Glycolysis1.05E-062.53E-031.05E-04YES
Heterotrimeric G-protein signaling pathway-rod outer segment phototransduction1.13E-051.29E-025.85E-04YES
TCA cycle3.09E-051.66E-023.42E-06YES
Wnt signaling pathway4.98E-052.87E-031.36E-02YES
PI3 kinase pathway1.00E-044.71E-031.21E-02YES
Cadherin signaling pathway4.14E-041.70E-051.23E-02YES
Hedgehog signaling pathway5.94E-041.66E-021.07E-02YES
5-Hydroxytryptamine degredation2.45E-034.90E-020.00E+00YES
Glutamine glutamate conversion1.80E-020.00E+000.00E+00YES
GABA-B_receptor_II_signaling4.89E-091.17E-021.83E-01
Beta3 adrenergic receptor signaling pathway7.87E-095.14E-021.34E-02
Unclassified3.31E-084.91E-014.76E-01
Alpha adrenergic receptor signaling pathway1.35E-071.98E-038.71E-02
Endogenous_cannabinoid_signaling6.67E-075.21E-021.83E-01
Axon guidance mediated by semaphorins1.46E-061.85E-035.27E-02
Endothelin signaling pathway1.86E-062.87E-032.12E-01
FGF signaling pathway2.41E-059.87E-022.00E-01
Integrin signalling pathway3.58E-055.21E-022.15E-03
T cell activation3.77E-051.70E-024.79E-01
B cell activation2.23E-047.26E-031.83E-01
Ras Pathway3.75E-044.91E-014.53E-01
De novo purine biosynthesis4.58E-047.28E-023.96E-05
Adrenaline and noradrenaline biosynthesis1.02E-035.21E-022.32E-02
Apoptosis signaling pathway3.07E-035.49E-014.72E-01
Angiogenesis3.07E-031.81E-014.76E-01
ATP synthesis3.30E-033.72E-011.89E-02
5HT3 type receptor mediated signaling pathway5.53E-031.03E-012.65E-02
VEGF signaling pathway7.86E-033.09E-014.79E-01
Pyrimidine Metabolism9.46E-034.27E-014.16E-01
PDGF signaling pathway9.46E-035.21E-028.88E-02
Ubiquitin proteasome pathway9.50E-036.13E-014.97E-01
Pentose phosphate pathway1.95E-025.80E-027.19E-02
Axon guidance mediated by Slit/Robo3.32E-021.23E-012.47E-01
Phenylethylamine degradation3.98E-021.72E-010.00E+00
Adenine and hypoxanthine salvage pathway3.98E-028.85E-037.19E-02
Alzheimer disease-amyloid secretase pathway4.95E-023.09E-018.71E-02
De novo pyrmidine ribonucleotides biosythesis7.11E-021.62E-021.81E-01
General transcription regulation7.55E-024.71E-039.08E-03
Phenylalanine biosynthesis7.69E-022.04E-014.16E-01
Arginine biosynthesis9.39E-024.97E-022.10E-01
Pyruvate metabolism1.02E-016.29E-013.35E-01
Circadian clock system1.21E-013.72E-012.10E-01
Tyrosine biosynthesis1.21E-012.04E-014.16E-01
Proline biosynthesis1.21E-016.13E-010.00E+00
FAS signaling pathway1.23E-015.49E-014.60E-01
Insulin/IGF pathway-protein kinase B signaling cascade1.55E-016.13E-012.80E-01
Oxidative stress response1.55E-011.03E-029.83E-04
Serine glycine biosynthesis1.65E-012.04E-010.00E+00
Asparagine and aspartate biosynthesis1.65E-012.04E-014.16E-01
Triacylglycerol metabolism1.77E-015.70E-010.00E+00
Anandamide_degradation1.77E-015.70E-010.00E+00
Fructose galactose metabolism2.05E-016.34E-014.79E-01
Gamma-aminobutyric acid synthesis2.10E-016.29E-014.16E-01
Heme biosynthesis2.37E-016.34E-010.00E+00
General transcription by RNA polymerase I2.72E-012.30E-011.83E-01
Axon guidance mediated by netrin2.88E-013.72E-015.22E-01
Interleukin signaling pathway2.92E-014.90E-013.31E-01
Blood coagulation2.92E-016.29E-016.34E-01
Sulfate assimilation2.97E-010.00E+007.24E-01
Pyridoxal phosphate salvage pathway2.97E-017.24E-010.00E+00
Aminobutyrate degradation2.97E-017.24E-017.24E-01
Purine metabolism2.97E-016.64E-014.16E-01
Hypoxia response via HIF activation3.20E-012.27E-011.89E-02
Toll receptor signaling pathway3.95E-016.34E-013.69E-01
Vitamin B6 metabolism4.02E-016.34E-010.00E+00
De novo pyrimidine deoxyribonucleotide biosynthesis4.35E-014.97E-022.10E-01
Alzheimer disease-presenilin pathway4.36E-011.66E-012.70E-01
TGF-beta signaling pathway4.36E-015.16E-015.37E-01
Formyltetrahydroformate biosynthesis4.36E-016.13E-014.16E-01
Androgen/estrogene/progesterone biosynthesis4.53E-015.18E-014.79E-01
Interferon-gamma signaling pathway4.53E-016.29E-015.43E-01
p53 pathway by glucose deprivation4.71E-015.21E-027.24E-01
Methylmalonyl pathway4.71E-017.24E-017.24E-01
Ascorbate degradation4.71E-015.70E-010.00E+00
Cell cycle5.06E-014.91E-014.79E-01
Cholesterol biosynthesis5.06E-016.64E-014.16E-01
p53 pathway feedback loops 25.35E-015.81E-011.84E-01
Salvage pyrimidine ribonucleotides5.44E-015.49E-014.16E-01
p53 pathway5.46E-015.81E-018.69E-02
DNA replication5.66E-013.16E-017.24E-01
mRNA splicing5.77E-011.62E-014.16E-01
Insulin/IGF pathway-mitogen activated protein kinase kinase/MAP kinase cascade5.77E-014.92E-013.35E-01
JAK/STAT signaling pathway5.77E-016.34E-017.24E-01
Transcription regulation by bZIP transcription factor5.77E-012.04E-012.80E-01
Xanthine and guanine salvage pathway5.77E-015.70E-017.24E-01
Coenzyme A biosynthesis5.77E-016.34E-012.31E-01
2-arachidonoylglycerol biosynthesis6.34E-010.00E+007.24E-01
Plasminogen activating cascade6.58E-012.04E-010.00E+00
N-acetylglucosamine metabolism6.58E-012.30E-014.16E-01
Mannose metabolism6.58E-011.00E-01#N/A
P53 pathway feedback loops 16.58E-016.34E-01#N/A
Notch signaling pathway6.71E-015.50E-015.22E-01
Folate biosynthesis6.99E-016.34E-01#N/A
5-Hydroxytryptamine biosynthesis6.99E-015.18E-01#N/A
Vitamin D metabolism and pathway7.49E-016.34E-017.24E-01
Salvage pyrimidine deoxyribonucleotides8.25E-01#N/A#N/A
O-antigen biosynthesis8.25E-016.34E-014.16E-01
Methylcitrate cycle8.25E-01#N/A#N/A
Vasopressin synthesis8.25E-012.27E-011.07E-01
Valine biosynthesis8.78E-013.66E-01#N/A
S adenosyl methionine biosynthesis8.78E-016.34E-014.16E-01
Ornithine degradation8.78E-01#N/A#N/A
Isoleucine biosynthesis8.78E-013.66E-01#N/A
Acetate utilization8.78E-016.34E-01#N/A
Threonine biosynthesis9.29E-015.18E-01#N/A
Thiamine metabolism9.29E-015.18E-014.16E-01
Succinate to proprionate conversion9.29E-016.34E-014.16E-01
PLP biosynthesis9.29E-015.18E-01#N/A
Lysine biosynthesis9.29E-016.34E-01#N/A
Lipoate_biosynthesis9.29E-016.34E-01#N/A
Leucine biosynthesis9.29E-015.18E-01#N/A
Carnitine metabolism9.29E-016.34E-014.16E-01
Carnitine and CoA metabolism9.29E-016.34E-014.16E-01
Histamine synthesis9.29E-016.34E-01#N/A
Alanine biosynthesis9.29E-015.18E-01#N/A
Bupropion_degradation9.41E-01#N/A#N/A
Methionine biosynthesis9.41E-01#N/A4.16E-01
Flavin biosynthesis9.41E-016.34E-014.16E-01
Cysteine biosynthesis9.41E-016.34E-01#N/A
Cobalamin biosynthesis9.41E-016.34E-01#N/A
Allantoin degradation9.41E-01#N/A#N/A

Supplementary Table 10. Analysis of dN/dS values from mouse and human PSD proteins.

dN, dS, dN/dS and median dN/dS values are given for proteins found in human and mouse cortical PSD, and proteins exclusive or significantly enriched to each species’ PSD. All values were obtained from Ensembl 62.

Ensembl Gene ID/ Mouse Ensembl Gene ID/ dNdS dN/dSMedian dN/dS Ensembl Gene ID/Human Ensembl Gene ID/ dNdSdN/dSMedian dN/dSEnsembl Gene ID/Mouse Ensembl Gene ID/dN/dSdN/dSMedian dN/dSEnsembl Gene ID/Mouse Ensembl Gene ID/dNdSdN/dSMedian dN/dSEnsembl Gene ID/Human Ensembl Gene ID/dN/dSdN/dSMedian dN/dSEnsembl Gene ID/Human Ensembl Gene ID/dN/dSdN/dSMedian dN/dS
Human PSD (Nat Neurosci. 2011 Jan;14(1):19-21) Mouse PSD Identified only in human PSD Identified only in mouse PSD Enriched in human PSD Enriched in mouse PSD
ENSG00000121083ENSMUSG0000002048300.081700.045432099ENSMUSG00000020483ENSG0000012108300.081700.041538096ENSG00000108518ENSMUSG000000182930.01880.21380.0879326470.067476115ENSG00000123091ENSMUSG000000285570.0030.11310.0265251990.049200877ENSMUSG00000004849ENSG0000010636700.652100.02032421ENSMUSG00000023944ENSG000000963840.00180.74890.00240.0352
ENSG00000197111ENSMUSG0000005685100.10430ENSMUSG00000056851ENSG0000019711100.10430ENSG00000108671ENSMUSG000000174280.00120.21410.005604858ENSG00000112531ENSMUSG0000006207800.14170ENSMUSG00000020149ENSG0000013806900.18420ENSMUSG00000004455ENSG000001862980.00140.42730.0033
ENSG00000124785ENSMUSG000000391140.01270.10580.120037807ENSMUSG00000039114ENSG000001247850.01270.10580.120037807ENSG00000123728ENSMUSG0000005002900.22570ENSG00000146006ENSMUSG000000718620.00850.15850.05362776ENSMUSG00000022884ENSG0000015697600.28330ENSMUSG00000021820ENSG000001486600.00090.27080.0033
ENSG00000123560ENSMUSG0000003142500.11470ENSMUSG00000028557ENSG000001230910.0030.11310.026525199ENSG00000175130ENSMUSG000000479450.02020.23480.086030664ENSG00000198492ENSMUSG000000400250.00170.16660.010204082ENSMUSG00000026797ENSG0000013685400.56460ENSMUSG00000072214ENSG000001847020.00441.17900.0037
ENSG00000107758ENSMUSG000000218160.00350.16030.021834061ENSMUSG00000031425ENSG0000012356000.11470ENSG00000153310ENSMUSG000000223780.00140.25680.005451713ENSG00000154001ENSMUSG000000210510.0010.16750.005970149ENSMUSG00000027438ENSG0000012581400.51540ENSMUSG00000025892ENSG000001525780.00150.38460.0039
ENSG00000070831ENSMUSG0000000669900.17230ENSMUSG00000062078ENSG0000011253100.14170ENSG00000141279ENSMUSG000000014410.01080.26520.040723982ENSG00000102081ENSMUSG000000008380.01360.19390.070139247ENSMUSG00000031425ENSG0000012356000.11470ENSMUSG00000043991ENSG000001851290.00120.27220.0044
ENSG00000138069ENSMUSG0000002014900.18420ENSMUSG00000071862ENSG000001460060.00850.15850.05362776ENSG00000099246ENSMUSG000000736390.00450.26690.016860247ENSG00000073921ENSMUSG000000393610.01140.21910.052031036ENSMUSG00000054459ENSG0000016303200.50230ENSMUSG00000026959ENSG000001768840.00410.74950.0055
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ENSMUSG00000046691ENSG000001789281.095.37770.202688882
ENSMUSG00000058773ENSG000001843570.04216.17290.006820133
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© G2C 2014. The Genes to Cognition Programme received funding from The Wellcome Trust and the EU FP7 Framework Programmes:
EUROSPIN (FP7-HEALTH-241498), SynSys (FP7-HEALTH-242167) and GENCODYS (FP7-HEALTH-241995).

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