Table 2.
Statistically significant KEGG signaling pathways identified from 1035 phosphoproteins in NFPAs. Count means the number of genes enriched in this pathway
| Category | Pathway name | Count | % | Fold enrichment | P value | Benjamini | Gene name of phosphoprotein |
|---|---|---|---|---|---|---|---|
| KEGG_PATHWAY | hsa03040:Spliceosome | 32 | 3.41 | 4.57 | 8.32E-13 | 1.83E-10 | SRSF1, NCBP1, CHERP, SRSF10, TRA2A, WBP11, CTNNBL1, SF3B1, DDX23, RBM8A, PCBP1, USP39, ACIN1, HNRNPC, PRPF40B, RBM25, PRPF40A, DDX42, SNW1, PRPF3, HNRNPA1, SF3A1, HNRNPU, SRSF2, SRSF7, SRSF6, SRSF9, SNRNP200, SLU7, PRPF38B, THOC1, RBM17 |
| KEGG_PATHWAY | hsa04611:Platelet activation | 22 | 2.35 | 3.22 | 3.32E-06 | 3.65E-04 | TLN1, LYN, TLN2, STIM1, ARHGAP35, MYL12B, PRKG1, ARHGEF12, ITPR1, ITPR2, AKT1, MAPK1, FGA, FGB, GP1BB, MAPK3, PPP1R12A, GP1BA, GNAS, PRKACB, SNAP23, ITGA2B |
| KEGG_PATHWAY | hsa03013:RNA transport | 24 | 2.56 | 2.65 | 2.89E-05 | 2.12E-03 | CLNS1A, NCBP1, NUP98, EIF5B, RNPS1, NUP155, SMN1, PNN, PABPC4L, EIF4B, EIF4G1, EIF3CL, EIF4G2, EIF4G3, NUP214, EIF3B, EIF3G, RAE1, RBM8A, SRRM1, ACIN1, RANBP2, THOC1, EIF2B5 |
| KEGG_PATHWAY | hsa04144:Endocytosis | 28 | 2.99 | 2.21 | 1.40E-04 | 7.70E-03 | CHMP2A, USP8, ASAP2, PML, ASAP1, EPS15L1, ARFGEF2, CHMP2B, GBF1, VPS4B, DNAJC6, VPS4A, VPS35, EHD2, IQSEC1, GIT1, PARD6A, DNM3, FAM21A, EPS15, RABEP1, ARRB1, IGF2R, ACAP2, SH3KBP1, SNX12, BIN1, DNM1 |
| KEGG_PATHWAY | hsa04150:mTOR signaling pathway | 12 | 1.28 | 3.93 | 1.75E-04 | 7.67E-03 | PRKCA, EIF4B, AKT1, MAPK1, RPS6KA3, AKT1S1, BRAF, TSC2, MAPK3, PRKAA1, RRAGD, RPTOR |
| KEGG_PATHWAY | hsa04270:Vascular smooth muscle contraction | 16 | 1.71 | 2.60 | 1.11E-03 | 3.98E-02 | PRKCA, BRAF, CALD1, MRVI1, PRKCE, ARHGEF12, PRKG1, PRKCD, ITPR1, ITPR2, ARHGEF11, MAPK1, MAPK3, PPP1R12A, GNAS, PRKACB |
| KEGG_PATHWAY | hsa04130:SNARE interactions in vesicular transport | 8 | 0.85 | 4.47 | 1.62E-03 | 4.98E-02 | STX1A, STX4, SEC22B, VAMP4, BET1L, SNAP23, VAMP2, STX1B |
| KEGG_PATHWAY | hsa05205:Proteoglycans in cancer | 22 | 2.35 | 2.09 | 1.77E-03 | 4.75E-02 | PRKCA, BRAF, ARHGEF12, PDCD4, FLNA, PXN, ITPR1, ITPR2, AKT1, EIF4B, MAPK1, CTTN, ANK1, ANK2, ANK3, SOS1, MAPK3, PPP1R12A, CAMK2D, PRKACB, SLC9A1, FN1 |
| KEGG_PATHWAY | hsa04910:Insulin signaling pathway | 17 | 1.81 | 2.34 | 2.24E-03 | 5.34E-02 | PHKA2, IRS2, BRAF, PHKB, ACACA, RPTOR, AKT1, PRKAR2B, MAPK1, PRKAR2A, SLC2A4, SOS1, PRKAR1A, MAPK3, TSC2, PRKAA1, PRKACB |
| KEGG_PATHWAY | hsa04666:Fc gamma R-mediated phagocytosis | 12 | 1.28 | 2.71 | 4.21E-03 | 8.86E-02 | PRKCA, AKT1, MAPK1, LYN, MARCKSL1, MAPK3, ASAP2, ASAP1, MARCKS, PRKCE, BIN1, PRKCD |
| KEGG_PATHWAY | hsa04114:Oocyte meiosis | 14 | 1.49 | 2.40 | 5.18E-03 | 9.86E-02 | ANAPC1, YWHAZ, CDC23, YWHAE, SMC3, ITPR1, ITPR2, MAPK1, RPS6KA3, SLK, MAPK3, CAMK2D, PPP3CB, PRKACB |
| KEGG_PATHWAY | hsa04922:Glucagon signaling pathway | 13 | 1.39 | 2.50 | 5.39E-03 | 9.44E-02 | PHKA2, PHKB, PGAM1, ACACA, ITPR1, ITPR2, AKT1, SLC2A1, PPP3CB, CAMK2D, GNAS, PRKAA1, PRKACB |
| KEGG_PATHWAY | hsa04720:Long-term potentiation | 10 | 1.07 | 2.88 | 7.12E-03 | 1.14E-01 | PRKCA, MAPK1, RPS6KA3, BRAF, MAPK3, PPP3CB, CAMK2D, PRKACB, ITPR1, ITPR2 |
| KEGG_PATHWAY | hsa04962:Vasopressin-regulated water reabsorption | 8 | 0.85 | 3.46 | 7.37E-03 | 1.10E-01 | DYNC1LI1, STX4, DYNC1LI2, AVP, GNAS, PRKACB, VAMP2, DYNC1I2 |
| KEGG_PATHWAY | hsa04022:cGMP–PKG signaling pathway | 17 | 1.81 | 2.04 | 8.48E-03 | 1.17E-01 | MEF2C, IRS2, SLC8A2, MRVI1, PRKCE, VDAC2, PRKG1, ITPR1, ITPR2, VDAC1, ATP2B1, AKT1, MAPK1, ATP2B4, MAPK3, PPP1R12A, PPP3CB |
| KEGG_PATHWAY | hsa04510:Focal adhesion | 20 | 2.13 | 1.84 | 1.15E-02 | 1.47E-01 | PRKCA, TLN1, BRAF, TLN2, TNC, ARHGAP35, MYL12B, PXN, FLNA, VCL, AKT1, MAPK1, ARHGAP5, PAK2, SOS1, MAPK3, PPP1R12A, SPP1, FN1, ITGA2B |
| KEGG_PATHWAY | hsa04730:Long-term depression | 9 | 0.96 | 2.85 | 1.25E-02 | 1.50E-01 | PRKCA, MAPK1, BRAF, LYN, MAPK3, GNAS, PRKG1, ITPR1, ITPR2 |
| KEGG_PATHWAY | hsa04970:Salivary secretion | 11 | 1.17 | 2.43 | 1.41E-02 | 1.59E-01 | PRKCA, ATP2B1, ATP2B4, SLC12A2, GNAS, PRKACB, VAMP2, PRKG1, ITPR1, SLC9A1, ITPR2 |
| KEGG_PATHWAY | hsa04915:Estrogen signaling pathway | 12 | 1.28 | 2.30 | 1.42E-02 | 1.53E-01 | HSP90AB1, AKT1, MAPK1, HSP90AA1, FKBP5, SOS1, MAPK3, GNAS, PRKACB, PRKCD, ITPR1, ITPR2 |
| KEGG_PATHWAY | hsa04530:Tight junction | 11 | 1.17 | 2.40 | 1.52E-02 | 1.55E-01 | PARD6A, TJP1, CTTN, MYH11, MYL12B, MYH14, PRKCE, MYH9, TJP2, TJAP1, MYH10 |
| KEGG_PATHWAY | hsa04914:Progesterone-mediated oocyte maturation | 11 | 1.17 | 2.40 | 1.52E-02 | 1.55E-01 | HSP90AB1, ANAPC1, AKT1, MAPK1, CCNB3, RPS6KA3, HSP90AA1, BRAF, MAPK3, CDC23, PRKACB |
| KEGG_PATHWAY | hsa04141:Protein processing in endoplasmic reticulum | 17 | 1.81 | 1.91 | 1.56E-02 | 1.52E-01 | HSP90AB1, SEC31A, HSP90AA1, WFS1, RRBP1, NSFL1C, PDIA6, SEC62, CANX, STUB1, STT3B, HYOU1, DNAJB11, SIL1, DNAJC1, UBE2E2, SSR3 |
| KEGG_PATHWAY | hsa04540:Gap junction | 11 | 1.17 | 2.38 | 1.64E-02 | 1.52E-01 | PRKCA, MAPK1, TJP1, SOS1, MAPK3, GNAS, PRKACB, PRKG1, TUBA1B, ITPR1, ITPR2 |
| KEGG_PATHWAY | hsa04919:Thyroid hormone signaling pathway | 13 | 1.39 | 2.15 | 1.70E-02 | 1.52E-01 | PRKCA, AKT1, MAPK1, NCOA2, HDAC2, HDAC1, TSC2, MAPK3, SLC2A1, RCAN1, PRKACB, NCOR1, SLC9A1 |
| KEGG_PATHWAY | hsa05100:Bacterial invasion of epithelial cells | 10 | 1.07 | 2.44 | 2.03E-02 | 1.71E-01 | DNM3, CTTN, SEPT2, ARHGEF26, CTNNA1, DNM1, PXN, CTNNA2, FN1, VCL |
| KEGG_PATHWAY | hsa04912:GnRH signaling pathway | 11 | 1.17 | 2.30 | 2.03E-02 | 1.65E-01 | PRKCA, MAPK1, MAP3K3, SOS1, MAPK3, CAMK2D, GNAS, PRKACB, PRKCD, ITPR1, ITPR2 |
| KEGG_PATHWAY | hsa05132:Salmonella infection | 10 | 1.07 | 2.29 | 2.91E-02 | 2.21E-01 | MAPK1, DYNC1LI1, TJP1, DYNC1LI2, MAPK3, PKN2, KLC4, KLC2, FLNA, DYNC1I2 |
| KEGG_PATHWAY | hsa04010:MAPK signaling pathway | 21 | 2.24 | 1.58 | 4.26E-02 | 2.99E-01 | PRKCA, MEF2C, BRAF, TAOK2, TAOK1, GNG12, FLNA, AKT1, MAPK1, RPS6KA3, PAK2, MAP3K3, ARRB1, SOS1, MAPT, MAPK3, PPP3CB, HSPB1, MAPK8IP3, STMN1, PRKACB |
| KEGG_PATHWAY | hsa04068:FoxO signaling pathway | 13 | 1.39 | 1.84 | 4.82E-02 | 3.22E-01 | USP7, IRS2, SGK3, BRAF, RBL2, AKT1, MAPK1, CCNB3, SLC2A4, HOMER3, SOS1, MAPK3, PRKAA1 |
| KEGG_PATHWAY | hsa03015:mRNA surveillance pathway | 10 | 1.07 | 2.09 | 4.84E-02 | 3.14E-01 | PABPC4L, NCBP1, FIP1L1, CSTF3, RBM8A, SRRM1, RNPS1, ACIN1, CPSF2, PNN |
| KEGG_PATHWAY | hsa04810:Regulation of actin cytoskeleton | 18 | 1.92 | 1.63 | 4.90E-02 | 3.08E-01 | GIT1, BRAF, ARHGEF6, ARHGAP35, MYL12B, GNG12, ARHGEF12, PXN, VCL, MAPK1, PAK2, SOS1, MAPK3, PIKFYVE, PPP1R12A, SLC9A1, FN1, ITGA2B |