Table 12. KEGG pathway, GO:BP, GO:CC and GO:MF analysis of corresponding genes of the evolved rules from the three datasets.
Here, ‘satisfiable rule’ or SRule by some KEGG-pathway(i.e., Path)/GO:BP/GO:CC/GO:MF means that all the genes (i.e., antecedent) of the rule are occurred together in the pathway/Go-term.
| DS | Pathway/GO-BP/GO-CC/GO-MF | p-value | #Gene | Genes | #SRule | SRule ids | |
|---|---|---|---|---|---|---|---|
| DS1 | Path | hsa04120:Ubiquitin mediated proteolysis | 0.0386 | 7 | MGRN1, FBXO2, KLHL13, DDB2, RHOBTB2, MID1, UBE2S | 1 | rule id 5233 |
| GO:BP | GO:0022402 cell cycle process | 8.69E-10 | 34 | PRC1, BLM, TTK, PKMYT1, CEP55, AURKB, RHOU, GTSE1, SPC24, KIF2C, CDCA8, NCAPH, NCAPG, CENPA, SKA1, ZWILCH, TXNL4B, CDK1 etc. | 21 | rule id 327, 2231, 2232, 2914, 7360 etc. | |
| GO:0000278 mitotic cell cycle | 1.02E-11 | 30 | PRC1, BLM, TTK, PKMYT1, SPC24, KIF15, BIRC5, CENPE, NDC80, SMC2, CDK2, MAD2L1, TIMELESS, PLK1, BUB1B, SETD8 etc. | 19 | rule id 327, 2231, 2232, 2914, 7360 etc. | ||
| GO:0022403 cell cycle phase | 6.04E-12 | 32 | PRC1, BLM, TTK, PKMYT1, CEP55, AURKB, RHOU, GTSE1, BIRC5, CENPE, NDC80, SMC2, CDK2, MAD2L1, TIMELESS, PLK1, BUB1B, RAD54B etc. | 18 | rule id 327, 2231, 2232, 2914, 7360 etc. | ||
| GO:0007017 microtubule-based process | 4.86E-04 | 14 | KIF11, PRC1, KIF15, KIF18B, TTK, NDC80, CENPE, MID1, MARK1, GTSE1, KIF2C, CENPA, BUB1B, KIF13B | 17 | rule id 327, 2232, 7360 etc. | ||
| GO:CC | GO:0043228 non-membrane-bounded organelle | 5.43E-05 | 70 | MTSS1, FOSL2, PRC1, CEP78, TTK, AURKB, SENP5, RHOU, GTSE1, SLC1A4, KIF2C, CDCA8, FRMD6, PBXIP1, FANCI, SNTB1, KIF13B, CDK1, MYO6, KIF11 etc. | 85 | rule id 151, 253, 298, 327, 415, 888, 1261, 1462, 1970, 2232 etc. | |
| GO:0043232 intracellular non-membrane-bounded organelle | 5.43E-05 | 70 | MTSS1, FOSL2, PRC1, CEP78, TTK, AURKB, SENP5, RHOU, GTSE1, SLC1A4, KIF2C, CDCA8, FRMD6 etc. | 85 | rule id 151, 253, 298, 327, 415, 888, 1261, 1462, 1970, 2232 etc. | ||
| GO:0044459 plasma membrane part | 0.0128 | 52 | DLC1, IL27RA, TSPAN4, RHOU, SLC1A4, FRMD6, CD44, LTB4R, SNTB1, CEACAM6, SLC22A3, RAB27A, ARHGEF4, ICAM1, PLD1, MYO6, LIFR etc. | 36 | rule id 212, 625, 1876, 6051 etc. | ||
| GO:MF | GO:0000166 nucleotide binding | 0.0015 | 56 | ACOX2, CTPS, PKMYT1, TTK, AURKB, RHOU, KIF2C, MCM8, LTB4R, ACAD8, RAB27B, ACAD9, RAB27A, KIF13B, NMNAT3, CDK1, MYO6, KIF11, LIMK2, KIF15, MCM4, MBD1, MCM5, CDK2, etc. | 51 | rule id 254, 327, 339, 344, 494, 639, 643 etc. | |
| GO:0001883 purine nucleoside binding | 4.95E-04 | 45 | ACOX2, FGFR2, BLM, CTPS, TTK, PKMYT1, AURKB, ADA, KIF2C, IGF1R, MCM8, STK32A, ACAD8, ACAD9, KIF13B, MYO5C, NMNAT3, CDK1, MYO6, KIF11, MKI67, LIMK2, KIF15, ATP11B etc. | 39 | rule id 254, 327, 339, 344, 494, 639, 643 etc. | ||
| GO:0001882 nucleoside binding | 5.72E-04 | 45 | ACOX2, FGFR2, BLM, CTPS, TTK, PKMYT1, AURKB, ADA, KIF2C, IGF1R, MCM8, STK32A, ACAD8, ACAD9, KIF13B, MYO5C, NMNAT3, CDK1, MYO6, KIF11, MKI67, LIMK2, IPPK, UBE2S, ABCC5 etc. | 39 | rule id 254, 327, 339, 344, 494, 639, 643 etc. | ||
| DS2 | Path | hsa00982:Drug metabolism | 9.79E-04 | 5 | GSTA4, FMO2, AOX1, GSTO2, MGST1 | 1 | rule id 12 |
| BP | GO:0042127 regulation of cell proliferation | 0.0341 | 9 | CEBPA, TNFSF4, BAX, SERPINE1, LIFR, IGF2, JAG1, CD24, PRL | 4 | rule id 78, 95, 145, 390 | |
| GO:0032583 regulation of gene-specific transcription | 0.0039 | 5 | CEBPA, TNFSF4, SMARCB1, PSRC1, IGF2 | 3 | rule id 52, 78, 225 | ||
| CC | GO:0005576 extracellular region | 0.0015 | 20 | TNFSF4, EGFL6, MMP9, APOC1, LIFR, GGH, IGF2, JAG1, MMP2, CHRDL1, PRRG1, PTGDS, C1QTNF4, SERPINE1, PECAM1, SERPINA3, C1QL1, GDF15, GFOD1, PRL | 6 | rule id 50,81,82,87,95,246 | |
| DS3 | Path | hsa04060:Cytokine-cytokine receptor interaction | 1.69E-04 | 12 | EGFR, IFNA21, CCR1, TNFSF12, IFNA1, IL23A, IL20RA, CCL3L1, INHBE, TNFRSF18, TNFSF12-TNFSF13, IFNGR2, IFNA17 | 1 | rule id 177 |
| GO:BP | GO:0006952 defense response | 1.88E-09 | 29 | IFNA21, S100A8, CCR1, BNIP3, HTN3, CD74, CFHR1, APOA4, REG3A, IFNA1, IL23A, SAA2, CCL3L1, SAA1, REG3G, CFHR5, IL1RL1, DEFB103A, SCUBE1, RNASE6 etc. | 12 | rule id 7, 144, 613, 617, 653, 654, 784, 822, 1067, 1182, 2293, 2342 | |
| GO:0006955 immune response | 8.71E-04 | 20 | FYB, IL1RL1, SLA2, CCR1, IGJ, CD300E, BNIP3, TNFSF12, C4BPA, CD74, CLEC4M, APOA4, CFHR1, CYBA, IL23A, CCL3L1, LYST, DEFA1, TNFSF12-TNFSF13, TREM1, CFHR5 | 12 | rule id 7, 349, 350, 351, 387, 654, 784, 1182, 1674, 2293, 2342, 2361 | ||
| GO:0003012 muscle system process | 0.0048 | 8 | CYBA, CALD1, MYH3, SLMAP, MYH4, ACTN2, SCN5A, CASQ2 | 4 | rule id 47, 138, 333, 2296 | ||
| GO:0006936 muscle contraction | 0.0118 | 7 | CALD1, MYH3, SLMAP, MYH4, ACTN2, SCN5A, CASQ2 | 4 | rule id 47, 138, 333, 2296 | ||
| GO:CC | GO:0005886 plasma membrane | 0.0090 | 67 | TEX101, STEAP4, NEURL, LHCGR, F2RL1, FCRL2, TNFSF12, KCNIP4, CALB2, FCRL3, APOB, SLMAP, ERAS, CALCRL, IFNGR2, EGFR, BSG, SLA2, SCUBE1, ACTN2, CACNG3, OR1D2, FLNA, TRPM2 etc. | 91 | rule id 126, 144, 155, 272, 321, 338, 339, 351, 385, 416 etc. | |
| GO:0044459 plasma membrane part | 0.0112 | 43 | PKHD1, CCR1, LHCGR, F2RL1, TRHR, PANX3, CLDN11, TNFSF12, CD74, CALB2, SORBS3, SLMAP, TEK, ERAS, CALCRL, IFNGR2, SCN5A, EGFR, TRPM2, KCNK3, CLEC4M etc. | 43 | rule id 27, 28, 126, 144, 301, 339, 351, 385, 513, 514 etc. | ||
| GO:0005576 extracellular region | 4.55E-09 | 59 | IFNA21, LHCGR, MMP27, TNFSF12, HTN3, APOA4, CFHR1, CFHR2, REG3A, APOB, OLFML3, SAA2, SERPINE2, SAA1, CCL3L1, CREG1, ANGPT1, REG3G, CFHR5, EGFR, NODAL, DEFA1 etc. | 40 | rule id 151, 180, 191, 346, 349, 350, 351, 486, 515, 517 etc. | ||
| GO:MF | GO:0046983 protein dimerization activity | 0.0029 | 16 | EGFR, S100A16, SCUBE1, TRHR, LHCGR, NFS1, BNIP3, DSCAML1, ACTN2, FLNA, APOA4, CYBA, APOB, BOK, TFAP2E, CRYBB2 | 3 | rules 1040, 1176, 2358 | |
| GO:0019955 cytokine binding | 0.0112 | 6 | IL1RL1, IL20RA, CCR1, TNFRSF18, IFNGR2, CD74 | 2 | rule id 177, 2342 |