Table 1 Identified Gene Ontology (GO) enrichment pathways of total protein hits across proteomic analyses. Identified pathways (nodes) are sorted by analysis (WT vs Pyk2^−/− and PS19^0/+ vs PS19^0/+;Pyk2^−/−) and by percent associated genes. Common pathways between analyses are bolded

Total Protein

WT vs Pyk2^−/−

6.10

ABCD2, ACADS, ACAT1, CNR1, ETFB

5

fatty acid beta-oxidation

GO:0006635

7.55E-05

0.007321993

6.06

ABCD2, CDC42, DBNL, DLG4, EPHA4, KIF1A

6

neuron projection organization

GO:0106027

1.45E-05

0.001450712

4.92

ACTN1, ARF6, CDC42, DBNL, DLG1, DLG4, EPHA4, KIF1A, PTPRS

9

postsynapse organization

GO:0099173

5.63E-07

5.68E-05

3.90

CDC42, DBNL, DLG4, EPHA4, KIF1A, MAP 6

6

dendrite morphogenesis

GO:0048813

1.72E-04

0.015991856

3.10

AAK1, AP2M1, ARF6, ATAD1, CDC42, DLG4, TF

7

regulation of endocytosis

GO:0030100

2.03E-04

0.018696253

3.02

ARF6, CDC42, DBNL, DLG4, EPHA4, KIF1A, MAP 6, PTPRS

8

dendrite development

GO:0016358

8.42E-05

0.008083191

2.75

CNR1, DLG1, DLG2, DLG4, GRIA2, SCN1B, SCN8A, SCN9A

8

voltage-gated ion channel activity

GO:0005244

1.61E-04

0.015097501

2.12

ARF6, BRSK1, CNR1, CNTN1, DBNL, EPHA4, KIF1A, MAP 6, PTPRS, SCN1B

10

regulation of neuron projection development

GO:0010975

2.05E-04

0.018639542

1.79

BRSK1, CDC42, CSPG5, DBNL, DLG4, EPHA4, ITSN2, KIF1A, MAP 6, OLFM1, PTPRS, SCN1B, SYT2

13

cell projection morphogenesis

GO:0048858

1.22E-04

0.011542529

1.73

ACTN1, ACTN4, CAB39, CAND1, CNR1, CSPG5, DBNL, DDOST, EEF2, HABP4, MLEC, PYGB, SYT2, TF, UBR4

15

regulated exocytosis

GO:0045055

4.99E-05

0.004892033

1.73

ACTN1, ACTN4, CAB39, CAND1, CHMP6, CNR1, CSPG5, DBNL, DDOST, EEF2, HABP4, MLEC, NSF, PYGB, SYT2, TF, UBR4

17

exocytosis

GO:0006887

1.48E-05

0.001465131

1.72

ARF6, BRSK1, CDC42, CNR1, CNTN1, DBNL, EPHA4, KIF1A, MAP 6, PTPRS, SCN1B, SEPTIN7

12

regulation of plasma membrane bounded cell projection organization

GO:0120035

3.24E-04

0.029116126

1.69

BRSK1, CDC42, DBNL, DLG4, EPHA4, ITSN2, KIF1A, MAP 6, OLFM1, PTPRS, SCN1B, SYT2

12

neuron projection morphogenesis

GO:0048812

3.68E-04

0.032738513

1.40

ARF6, BRSK1, CDC42, CNR1, CNTN1, DBNL, DLG4, EPHA4, ITSN2, KIF1A, MAP 6, OLFM1, PTPRS, SCN1B, SYT2

15

neuron projection development

GO:0031175

5.08E-04

0.044721907

PS19^0/+ vs PS19^0/+;Pyk2^−/−

10.34

DLG2, DLG4, MINK1, NLGN3, NPTX1, OPRM1, PRRT1, PTK2B, SRC

9

regulation of neurotransmitter receptor activity

GO:0099601

8.49E-08

2.16E-05

9.88

DLG2, DLG4, GRIK4, MINK1, NLGN3, OPRM1, PRRT1, PTK2B

8

ionotropic glutamate receptor activity

GO:0004970

6.51E-07

1.62E-04

8.26

ABCA2, C1QA, CD9, DMD, GFAP, GRN, GSTP1, PRDX6, SIRT2, TSPAN2

10

glial cell development

GO:0021782

1.38E-07

3.48E-05

7.76

DLG2, DLG4, GRIK4, MINK1, NLGN3, OPRM1, PLCB1, PRRT1, PTK2B

9

glutamate receptor signaling pathway

GO:0007215

1.01E-06

2.51E-04

7.09

ABCA2, CD9, HEXB, MTOR, PRDX6, PTN, SCN2A, SIRT2, TSPAN2, UGT8

10

myelination

GO:0042552

5.76E-07

1.44E-04

6.67

DMD, PLCB1, PTN, PTPRS, RAB1B, RAP1B, RAP2B, TJP2

8

endothelial cell differentiation

GO:0045446

1.27E-05

0.003012572

5.88

APOE, DLG4, FLOT1, GFAP, LGI1, NLGN3, PRRT1, PTK2B, PTN, SYT12

10

positive regulation of synaptic transmission

GO:0050806

3.17E-06

7.63E-04

5.75

APBB1, APOE, CNTN1, DMD, EHD1, GRN, MTOR, OPA1, PTK2B, PTN

10

positive regulation of neuron projection development

GO:0010976

3.90E-06

9.36E-04

5.34

APOE, CPEB3, CPLX2, DLG4, ERC2, GFAP, PRRT1, PTK2B, PTN, SYT12, VGF

11

regulation of synaptic plasticity

GO:0048167

2.59E-06

6.30E-04

5.06

ABCA2, C1QA, CD9, DMD, GFAP, GRN, GSTP1, MTOR, PRDX6, PTN, SIRT2, TSPAN2

12

glial cell differentiation

GO:0010001

1.57E-06

3.84E-04

5.02

APOE, CPEB3, CPLX2, DLG4, ERC2, FABP5, FLOT1, GFAP, GRIK4, LGI1, MTOR, NLGN3, NPTX1, NTNG1, PLCB1, PRRT1, PTK2B, PTN, PTPRS, RAP1B, SRC, SYT12, VGF

23

regulation of trans-synaptic signaling

GO:0099177

2.19E-11

5.74E-09

4.63

DLG2, DLG4, DMD, GRIK4, MINK1, NLGN3, OPRM1, PRRT1, PTK2B, RYR1

10

ligand-gated cation channel activity

GO:0099094

2.59E-05

0.006110782

4.48

APOE, CALR, CPEB3, EDC4, LARP1, PIN1, PURA, RACK1, RTN1, UPF1

10

negative regulation of cellular amide metabolic process

GO:0034249

3.40E-05

0.007919981

4.42

ABCA2, C1QA, CD9, DMD, GFAP, GRN, GSTP1, HEXB, MTOR, PRDX6, PTK2B, PTN, SIRT2, TSPAN2

14

gliogenesis

GO:0042063

1.06E-06

2.62E-04

4.20

APOE, CALR, CSNK2B, GRN, MTOR, PLPP3, PPM1F, PTK2B, PTN, SRC

10

regulation of epithelial cell migration

GO:0010632

5.89E-05

0.013542207

3.60

APBB1, APOE, CNTN1, DGKG, DMD, EHD1, FKBP4, GFAP, GRN, MTOR, NTNG1, OPA1, PKN1, PTK2B, PTN, PTPRS, THY1

17

regulation of neuron projection development

GO:0010975

1.23E-06

3.02E-04

3.59

APOE, CPEB3, CPLX2, DLG2, DLG4, ERC2, FLOT1, GFAP, GRIK4, LGI1, LIN7A, MINK1, MTOR, NLGN3, NPTX1, NTNG1, OPRM1, PLCB1, PRRT1, PTK2B, PTN, PTPRS, RAP1B, SLC18A3, SRC, SYPL1, SYT12, VGF

28

chemical synaptic transmission

GO:0007268

3.09E-10

8.07E-08

3.58

CADM4, CD81, CNTN1, DLG4, MTOR, PTK2B, RACK1, RAP2B, SRC, THY1

10

regulation of peptidyl-tyrosine phosphorylation

GO:0050730

2.17E-04

0.048624534

3.54

APOE, CALR, CSNK2B, GRN, MTOR, PKN1, PLPP3, PPM1F, PTK2B, PTN, SRC

11

epithelial cell migration

GO:0010631

1.18E-04

0.026898848

3.45

APBB1, APOE, CNTN1, DLG4, DMD, EHD1, GRN, MTOR, OPA1, PKN1, PTK2B, PTN, SRC

13

positive regulation of cell projection organization

GO:0031346

3.66E-05

0.008487912

3.37

ARL6, ARPC5, CLIP1, FKBP4, GRB2, MTOR, OPA1, PIN1, PKN1, PTK2B, TPPP3

11

protein polymerization

GO:0051258

1.78E-04

0.040236304

3.22

APBB1, APOE, FLOT1, GRB2, GRN, LGI1, NLGN3, NPTX1, NTNG1, OLFM1, PKN1, PTN, PTPRS, RHOG, S100A6, SRC, THY1, TSPAN2

18

axon development

GO:0061564

2.88E-06

6.96E-04

3.19

AMPD3, ARPC5, BIN2, CPLX2, CSNK2B, CTSA, DDOST, FABP5, GRN, GSTP1, HEXB, PA2G4, PRDX6, PTGES2, RAB6A, RAP1B, RAP2B, RHOG, VAT1

19

leukocyte degranulation

GO:0043299

1.73E-06

4.23E-04

3.16

AMPD3, ANXA5, ARPC5, ATP9A, BIN2, CD9, CPLX2, CSNK2B, CTSA, DDOST, ERC2, FABP5, GRN, GSTP1, HABP4, HEXB, LIN7A, PA2G4, PKN1, PRDX6, PTGES2, RAB6A, RAP1B, RAP2B, RHOG, SYT12, SYT17, TLN1, VAT1, VPS4A, VTI1B

31

exocytosis

GO:0006887

7.34E-10

1.90E-07

3.12

APOE, ARPC5, CLIP1, CRYAB, FKBP4, GFAP, GRB2, IRGM, MTOR, PKN1, PTK2B, RACK1, RAP1B, SRC, TPPP3

15

regulation of protein-containing complex assembly

GO:0043254

2.93E-05

0.006858316

3.12

AMPD3, ANXA5, ARPC5, BIN2, CD9, CPLX2, CSNK2B, CTSA, DDOST, ERC2, FABP5, GRN, GSTP1, HABP4, HEXB, PA2G4, PRDX6, PTGES2, RAB6A, RAP1B, RAP2B, RHOG, SYT12, SYT17, TLN1, VAT1, VTI1B

27

regulated exocytosis

GO:0045055

1.41E-08

3.61E-06

3.11

APBB1, APOE, DLG4, DMD, FLOT1, GRB2, LGI1, MINK1, NLGN3, NPTX1, NTNG1, OLFM1, OPA1, PKN1, PTN, PTPRS, RHOG, S100A6, SRC, SYT17, THY1, UGT8

22

neuron projection morphogenesis

GO:0048812

3.78E-07

9.50E-05

2.97

APBB1, APOE, DLG4, FLOT1, GRB2, LGI1, MINK1, NLGN3, NPTX1, NTNG1, OLFM1, OPA1, PKN1, PTN, PTPRS, RHOG, S100A6, SRC, THY1

19

cell morphogenesis involved in neuron differentiation

GO:0048667

4.88E-06

0.001166078

2.95

CALR, CPEB3, EDC4, EEF1D, EEF1G, EIF3B, HABP4, LARP1, MTOR, PA2G4, PTK2B, PURA, RACK1, UPF1

14

regulation of translation

GO:0006417

9.95E-05

0.022778961

2.94

APBB1, APOE, FLOT1, GRB2, LGI1, NLGN3, NPTX1, NTNG1, OLFM1, PKN1, PTPRS, RHOG, S100A6, SRC, THY1

15

axonogenesis

GO:0007409

5.71E-05

0.013191499

2.79

APBB1, APOE, C1QA, CNTN1, CPEB3, DGKG, DLG4, DMD, EHD1, FKBP4, FLOT1, GFAP, GPM6B, GRB2, GRN, LGI1, MINK1, MTOR, NLGN3, NPTX1, NTNG1, OLFM1, OPA1, PKN1, PTK2B, PTN, PTPRS, RHOG, S100A6, SRC, SYT17, THY1, TSPAN2, UGT8

34

neuron development

GO:0048666

2.33E-09

6.02E-07

2.78

ABCA2, APOE, CADM4, DMD, GSTP1, MTOR, PKN1, PLPP3, PPM1F, PPME1, PTN, RACK1, SIRT2, THY1

14

negative regulation of phosphate metabolic process

GO:0045936

1.84E-04

0.041490973

2.72

APBB1, APOE, CNTN1, DGKG, DMD, EHD1, FKBP4, GFAP, GRN, MTOR, NTNG1, OPA1, PKN1, PTK2B, PTN, PTPRS, RHOG, SRC, THY1

19

regulation of plasma membrane bounded cell projection organization

GO:0120035

1.66E-05

0.003934112

2.58

APCS, APOE, CADM4, CALR, CNTN1, CPEB3, CRYAB, CTSA, DMD, EDC4, ERC2, FLOT2, GSTP1, LARP1, MTOR, OGT, PFDN1, PIN1, PKN1, PLPP3, PPM1F, PPME1, PTN, PURA, RACK1, RTN1, SIRT2, SRC, THY1, UPF1

30

negative regulation of protein metabolic process

GO:0051248

1.41E-07

3.55E-05

2.46

ABCA2, APBB1, APOE, C1QA, CALR, CD9, CNTN1, CPEB3, DGKG, DLG4, DMD, EHD1, FKBP4, FLOT1, GFAP, GPM6B, GRB2, GRN, GSTP1, HEXB, LGI1, MINK1, MTOR, NLGN3, NPTX1, NTNG1, OLFM1, OPA1, OPRM1, PIN1, PKN1, PRDX6, PTK2B, PTN, PTPRS, RHOG, S100A6, SIRT2, SRC, SYT17, THY1, TSPAN2, UGT8

43

neurogenesis

GO:0022008

5.77E-10

1.50E-07

2.43

APBB1, APOE, C1QA, CALR, CNTN1, CPEB3, DGKG, DLG4, DMD, EHD1, FKBP4, FLOT1, GFAP, GPM6B, GRB2, GRN, LGI1, MINK1, MTOR, NLGN3, NPTX1, NTNG1, OLFM1, OPA1, PIN1, PKN1, PTK2B, PTN, PTPRS, RHOG, S100A6, SRC, SYT17, THY1, TSPAN2, UGT8

36

neuron differentiation

GO:0030182

2.77E-08

7.09E-06

2.37

APOE, CALR, CD81, CD9, CNTN1, CSNK2B, GRN, GSTP1, MINK1, MTOR, NTNG1, PKN1, PLCB1, PLPP3, PPM1F, PTK2B, PTN, RACK1, RAP2B, RHOG, SRC, THY1

22

regulation of cell migration

GO:0030334

2.87E-05

0.006756045

2.33

APBB1, APOE, C1QA, CALR, CNTN1, CPEB3, DGKG, DLG4, DMD, EHD1, FKBP4, FLOT1, GFAP, GPM6B, GRB2, GRN, LGI1, MINK1, MTOR, NLGN3, NPTX1, NTNG1, OLFM1, OPA1, OPRM1, PIN1, PKN1, PTK2B, PTN, PTPRS, RHOG, S100A6, SIRT2, SRC, SYT17, THY1, TSPAN2, UGT8

38

generation of neurons

GO:0048699

3.20E-08

8.16E-06

2.11

APOE, CADM4, CALR, CPEB3, CRYAB, DMD, EDC4, ERC2, GSTP1, LARP1, MTOR, OGT, PKN1, PLPP3, PPM1F, PPME1, PTN, PURA, RACK1, SIRT2, SRC, THY1, UPF1

23

negative regulation of cellular protein metabolic process

GO:0032269

1.53E-04

0.034655683