Table 5.
Functional characteristics of 130 overlapped molecules between phosphoproteins and invasive DEGs in NFPAs, clustered with GO and KEGG pathway enrichments. Count means the number of genes enriched in each item
| Category | Functional characteristics | Count | % | Fold enrichment | P value | Gene name of overlapped molecule |
|---|---|---|---|---|---|---|
| Annotation cluster 1 | ||||||
| GOTERM_CC_DIRECT | GO:0005913~cell–cell adherens junction | 11 | 8.73 | 5.05 | 6.35E-05 | ALDOA, TNKS1BP1, LIMA1, PGM5, CALD1, ASAP1, EPS15L1, H1FX, NDRG1, PLEC, CHMP2B |
| GOTERM_BP_DIRECT | GO:0098609~cell–cell adhesion | 10 | 7.94 | 5.16 | 1.34E-04 | ALDOA, TNKS1BP1, LIMA1, CALD1, ASAP1, EPS15L1, H1FX, NDRG1, PLEC, CHMP2B |
| GOTERM_MF_DIRECT | GO:0098641~cadherin binding involved in cell–cell adhesion | 10 | 7.94 | 4.73 | 2.58E-04 | ALDOA, TNKS1BP1, LIMA1, CALD1, ASAP1, EPS15L1, H1FX, NDRG1, PLEC, CHMP2B |
| Annotation cluster 2 | ||||||
| KEGG_PATHWAY | hsa04611:Platelet activation | 10 | 7.94 | 10.58 | 2.53E-07 | AKT1, TLN2, STIM1, GNAS, SNAP23, PRKG1, ARHGEF12, ITPR1, ITPR2, ITGA2B |
| Annotation cluster 3 | ||||||
| GOTERM_MF_DIRECT | GO:0005085~guanyl-nucleotide exchange factor activity | 6 | 4.76 | 6.98 | 1.66E-03 | NGEF, ARHGEF6, DOCK7, ARHGEF12, DOCK11, ARHGEF11 |
| GOTERM_BP_DIRECT | GO:0043547~positive regulation of GTPase activity | 12 | 9.52 | 2.97 | 2.25E-03 | NGEF, ARHGEF6, TSC2, ASAP2, ASAP1, GNAS, ARHGEF12, CDC42EP4, DOCK11, ARHGEF11, STXBP5L, SPTB |
| GOTERM_MF_DIRECT | GO:0005089~Rho guanyl-nucleotide exchange factor activity | 5 | 3.97 | 8.91 | 2.34E-03 | NGEF, ARHGEF6, ARHGEF12, DOCK11, ARHGEF11 |
| GOTERM_MF_DIRECT | GO:0005096~GTPase activator activity | 8 | 6.35 | 3.94 | 4.17E-03 | ARHGEF6, TSC2, ASAP2, ASAP1, ARHGEF12, CDC42EP4, ARHGEF11, STXBP5L |
| GOTERM_BP_DIRECT | GO:0051056~regulation of small GTPase mediated signal transduction | 5 | 3.97 | 5.22 | 1.52E-02 | NGEF, ARHGEF6, TSC2, ARHGEF12, ARHGEF11 |
| GOTERM_BP_DIRECT | GO:0035023~regulation of Rho protein signal transduction | 4 | 3.17 | 6.91 | 1.98E-02 | NGEF, ARHGEF6, ARHGEF12, ARHGEF11 |
| GOTERM_BP_DIRECT | GO:0043065~positive regulation of apoptotic process | 7 | 5.56 | 3.27 | 2.00E-02 | AKT1, NGEF, BCLAF1, ARHGEF6, ARHGEF12, GAL, ARHGEF11 |
| Annotation cluster 4 | ||||||
| GOTERM_MF_DIRECT | GO:0008017~microtubule binding | 6 | 4.76 | 3.96 | 1.76E-02 | KIF1A, MAP4, NDRG1, CLASP2, KIF16B, KIF13B |
| GOTERM_CC_DIRECT | GO:0005874~microtubule | 7 | 5.56 | 3.33 | 1.83E-02 | KIF1A, STIM1, MAP4, NDRG1, CLASP2, KIF16B, KIF13B |
| GOTERM_CC_DIRECT | GO:0005871~kinesin complex | 3 | 2.38 | 8.39 | 4.91E-02 | KIF1A, KIF16B, KIF13B |
| Annotation cluster 5 | ||||||
| GOTERM_BP_DIRECT | GO:0018107~peptidyl-threonine phosphorylation | 3 | 2.38 | 11.05 | 2.97E-02 | AKT1, STK39, PRKCD |
| GOTERM_MF_DIRECT | GO:0004672~protein kinase activity | 7 | 5.56 | 2.68 | 4.61E-02 | AKT1, AVP, CASK, STK39, PRKCD, CDK14, DCLK1 |
| Annotation cluster 6 | ||||||
| GOTERM_BP_DIRECT | GO:1903779~regulation of cardiac conduction | 4 | 3.17 | 10.00 | 7.32E-03 | SLC8A2, STIM1, ITPR1, ITPR2 |
| KEGG_PATHWAY | hsa04020:Calcium signaling pathway | 5 | 3.97 | 3.84 | 3.79E-02 | SLC8A2, STIM1, GNAS, ITPR1, ITPR2 |
| Annotation cluster 7 | ||||||
| KEGG_PATHWAY | hsa04611:Platelet activation | 10 | 7.94 | 10.58 | 2.53E-07 | AKT1, TLN2, STIM1, GNAS, SNAP23, PRKG1, ARHGEF12, ITPR1, ITPR2, ITGA2B |
| KEGG_PATHWAY | hsa04270:Vascular smooth muscle contraction | 8 | 6.35 | 9.41 | 1.64E-05 | CALD1, GNAS, PRKG1, ARHGEF12, PRKCD, ITPR1, ARHGEF11, ITPR2 |
| KEGG_PATHWAY | hsa04915:Estrogen signaling pathway | 6 | 4.76 | 8.34 | 6.44E-04 | AKT1, FKBP5, GNAS, PRKCD, ITPR1, ITPR2 |
| GOTERM_BP_DIRECT | GO:0050796~regulation of insulin secretion | 5 | 3.97 | 10.44 | 1.30E-03 | STX1A, MARCKS, GNAS, ITPR1, ITPR2 |
| KEGG_PATHWAY | hsa04922:Glucagon signaling pathway | 5 | 3.97 | 6.95 | 5.21E-03 | AKT1, ACACA, GNAS, ITPR1, ITPR2 |
| KEGG_PATHWAY | hsa04730:Long-term depression | 4 | 3.17 | 9.17 | 8.74E-03 | GNAS, PRKG1, ITPR1, ITPR2 |
| KEGG_PATHWAY | hsa05205:Proteoglycans in cancer | 6 | 4.76 | 4.13 | 1.34E-02 | AKT1, ANK1, ARHGEF12, ITPR1, PXN, ITPR2 |
| KEGG_PATHWAY | hsa04970:Salivary secretion | 4 | 3.17 | 6.40 | 2.30E-02 | GNAS, PRKG1, ITPR1, ITPR2 |
| KEGG_PATHWAY | hsa04540:Gap junction | 4 | 3.17 | 6.25 | 2.44E-02 | GNAS, PRKG1, ITPR1, ITPR2 |
| KEGG_PATHWAY | hsa04022:cGMP–PKG signaling pathway | 5 | 3.97 | 4.35 | 2.55E-02 | AKT1, SLC8A2, PRKG1, ITPR1, ITPR2 |
| KEGG_PATHWAY | hsa04912:GnRH signaling pathway | 4 | 3.17 | 6.05 | 2.66E-02 | GNAS, PRKCD, ITPR1, ITPR2 |
| KEGG_PATHWAY | hsa04750:Inflammatory mediator regulation of TRP channels | 4 | 3.17 | 5.62 | 3.22E-02 | GNAS, PRKCD, ITPR1, ITPR2 |
| KEGG_PATHWAY | hsa04020:Calcium signaling pathway | 5 | 3.97 | 3.84 | 3.79E-02 | SLC8A2, STIM1, GNAS, ITPR1, ITPR2 |
| GOTERM_BP_DIRECT | GO:0030168~platelet activation | 4 | 3.17 | 4.87 | 4.84E-02 | AKT1, PRKCD, ITPR1, ITPR2 |