Table 2.

Enrichment analysis report by process networks

Number	Networks	HCC1954 vs MCF10A (P value)	Genes
1	Cell cycle, S phase	6.7436787067153E-13	RFC4, TOP2 beta, Chk2, MCM3, SG2NA, NFBD1, Brca1, Cyclin B, Cyclin B2, CRM1, CHMP1A, ORC1L, MCM5, Nek2A, MCM4, PRIM2A, MCM10, ORC3L, DERPC, Histone H1.5, ChAF1 subunit B, ORC6L, ASK (Dbf4), POLA1, POLE2, FEN1, DNA ligase I, p21, RFC5, BUB1, Geminin, Sgo1, Rad51, DNA polymerase alpha/primase, PRIM1, HP1, Securin, CDK1 (p34), C-Nap1(CEP2), Ubiquitin, PCNA, CDC18L (CDC6), Cyclin A1, UHRF2, BRIP1, RFC3, POLD reg (p68), ATM, TOP2 alpha, POLE3-POLE4 complex, MCM6, POLA2, GADD45 alpha, RFC1, RFC2, Cyclin A, DNA polymerase sigma, PCTK1, TOP2, ZAK, Cdt1, Cyclin B1, POLE3 (YBL1), p53, RFC complex, Emi1, Nibrin, PKA-cat (cAMP-dependent), Rad21, RPA2, Histone H4, DCC1, Histone H1, CDC45L
2	DNA damage checkpoint	9.94791617812864E-08	RFC4, CIA/ASF1, p38alpha (MAPK14), Chk2, 14-3-3 epsilon, NFBD1, Brca1, Cyclin B, Cyclin B2, Cyclin D3, HUS1, CDC25C, ANAPC11, ERK1/2, Cyclin D, 14-3-3, Rad50, CDC25A, BTG2, p21, RFC5, Securin, CDK1 (p34), ANAPC7, Cyclin D2, Ubiquitin, PCNA, CDC23, Cyclin A1, MRE11, BRIP1, RFC3, MRN complex, FANCD2, RAD1, ATM, MDM2, GADD45 alpha, RFC1, Ku70, RFC2, Cyclin A, Cyclin D1, JNK(MAPK8-10), NF-kB, 14-3-3 eta, p38gamma (MAPK12), RUVBL2, p53, RFC complex, Bard1, USP1, Nibrin, p38 MAPK, Rad21
3	Cell cycle, mitosis	3.45421335237624E-07	Tubulin beta, Tubulin gamma, MIS12, HZwint-1, Cyclin B, Cyclin B2, ZW10, CAPZ beta, Nek2A, CDC25C, Tubulin alpha 1A, CENP-A, ANAPC11, MACF1, MAD2a, CENP-H, SPBC25, Importin (karyopherin)-alpha, Rod, RCC1, CAP-D2/D3, Kid, CDC25A, USP16, BUB1, MPP6, Dynamin-2, Aurora-A, Actin, CDC25, CDCA1, HP1, Securin, CDK1 (p34), SIL, ANAPC7, Ubiquitin, CDC23, PARP-2, Tubulin alpha, Dynein 1, cytoplasmic, heavy chain, Tctex-1, Survivin, Karyopherin alpha 2, MAPRE3(EB3), Dynamin-3, ANAPC10, DLC1 (Dynein LC8a), BUBR1, CAP-H/H2, NF45 (ILF2), Cyclin A, EML4, HEC, TTK, CAS-L, TOP2, MAD2L1BP, 14-3-3 eta, Dynamin, MCAK, Cyclin B1, PAFAH alpha (LIS1), RAE1, PARD6, HP1 gamma, Rad21, Zwilch, NSL1, Histone H1, Tubulin (in microtubules)
4	Cell cycle, G2-M	8.54322861724783E-07	TOP2 beta, p38alpha (MAPK14), Chk2, TCP1-theta, 14-3-3 epsilon, EGF, TCP1-delta, NFBD1, Brca1, Cyclin B, Cyclin B2, GRB2, HUS1, Nek2A, CDC25C, HIPK2, p38delta (MAPK13), EGFR, ANAPC11, NEDD8, MAD2a, ERK1/2, 14-3-3, Histone H1.5, Centrin-2, RCC1, Rad50, CAP-D2/D3, Kid, CDC25A, p21, BUB1, Rad51, CDK10, Aurora-A, CDC25, p90Rsk, Securin, CDK1 (p34), RINT-1, ANAPC7, Ubiquitin, FHIT, CDC23, Cyclin A1, Shc, CKS1, TRF1, FANCD2, ATM, AKT3, MRLC, Lamin B1, TCP1-epsilon, BUBR1, TOP2 alpha, CAP-H/H2, LATS2, Lamin B, IGF-1 receptor, GADD45 alpha, Cyclin A, CNAP1, PCTK1, TOP2, AKT(PKB), ZAK, 14-3-3 eta, Dynamin, BRRN1, p38gamma (MAPK12), Cyclin B1, p53, Emi1, p38 MAPK, PKA-cat (cAMP-dependent), MAT1, Histone H1
5	DNA damage, BER-NER repair	1.15885388728944E-06	RFC4, Chk2, OGG1, NEIL3, NFBD1, Brca1, PARP-1, HUS1, MBD4, NEIL1, ERCC6, Rad50, DNA polymerase beta, POLE2, XPF, FEN1, DNA ligase I, RFC5, TFIIH p52 subunit, TDG, TFIIH p34 subunit, PCNA, UNG1, PARP-2, MRE11, DDB2, RFC3, RAD23B, MRN complex, RAD1, POLD reg (p68), ATM, PARG, POLE3-POLE4 complex, RFC1, RFC2, Brca1/Bard1, PARP-3, POLE3 (YBL1), p53, RFC complex, Bard1, Nibrin, MBD1, XPD, RPA2, MAT1, TFB5
6	Cell adhesion, cell junctions	7.60204508182795E-06	Tubulin beta, Tiam1, VE-cadherin, BPAG2, N-cadherin, E-cadherin, ITGB1, 14-3-3 epsilon, Cingulin, MUPP1, Tcf(Lef), ZO-1, Fer, ERK1/2, Keratin 5, 14-3-3, Claudin-16, Beta-catenin, Nectin-2, BPAG1, DLG5(P-dlg), Connexin 46, Claudin-8, Desmoglein 3, Vimentin, Actin, Paxillin, MAGI-1(BAIAP1), GIT1, PI3K reg class IA (p85), JAM3, ATP1B1, Tubulin alpha, Desmocollin 3, R-cadherin, PKC, PLC-beta, Endothelin-1, CASK, Keratin 18, Desmoglein 2, Beta-fodrin, Claudin-7, Itch, PLC-gamma, Keratin 8/18, Claudin-4, SIP1 (ZFHX1B), Nectin-3, Desmoplakin, Keratin 8, ZO-3, PSD-95, Keratin 6A, PEZ, ERK2 (MAPK1), Caveolin-1, 14-3-3 eta, Claudin-3, PARD6, Connexin 31, Tubulin (in microtubules)
7	Cell cycle, core	0.000013064502255225	MCM3, p14ARF, Cyclin B, Cyclin B2, Cyclin D3, ZW10, ORC1L, MCM5, Nek2A, CDC25C, CENP-A, MCM4, MCM10, ORC3L, MAD2a, CENP-H, Cyclin D, Rod, Kid, CDC25A, ORC6L, ASK (Dbf4), FEN1, DNA ligase I, p21, BUB1, DNA polymerase alpha/primase, Aurora-A, Securin, CDK1 (p34), Cyclin E2, CDC18L (CDC6), Survivin, BUBR1, MCM6, Cyclin A, Cyclin D1, HEC, TOP2, Cdt1, Cyclin B1, p16INK4, Emi1, RPA2, Zwilch, MAT1, CDC45L
8	Cell adhesion, cadherins	0.0000405298162912831	RACK1, WNT4, VE-cadherin, BPAG2, N-cadherin, E-cadherin, ITGB1, PCDHA6, PCDHA4, VLDLR, Tcf(Lef), EGFR, Ski, ZO-1, Presenilin 1, Fer, DKK1, PCDHGC3, Casein kinase I epsilon, Beta-catenin, Nectin-2, H-cadherin, PTPR-mu, SSX2IP, BPAG1, DLG5(P-dlg), PCDHGB2, Desmoglein 3, Actin, CTNNAL1, Protocadherin 18, PCDHGA3, Shc, PI3K reg class IA (p85), PCDA7, Desmocollin 3, R-cadherin, MTSS1, Cadherin 10, FAT1, PKC, PCDHGA1, FHL2, PKC-alpha, Protocadherin gamma B1, Desmoglein 2, WNT, WNT10B, EVL, Nectin-3, LRP6, Axin2, Casein kinase I, PCDHGA12, Fyn, Vinexin, DAB1, PEZ, AKT(PKB), PDZK3, PCDHGB4, Axin, PTPR-zeta, Frizzled, Tubulin (in microtubules)
9	Proteolysis ubiquitin-proteasomal proteolysis	0.0000769830526795964	MDM4, HAUS7, Brca1, PSMB8(LMP7), KEAP1, PSMA4, Cullin 2, c-Cbl, UBCH7, UCHL3, SAE1/2, TGT, PSMB1, PSMC3, PSMC6, PSMD5, PSMA7, PSMC4, SENP2, SAE1, GRAIL, PSMD10 (Gankyrin), PSME1, DTX3, Ubiquitin, PSMD3, PSMD2, RAD23B, NF-X1, PSMB6, MUF1, PSME2, PSMD8, PSMD7, Syntaxin 5, Itch, Elongin C, MPDZ, NEDD4L, MDM2, DORFIN, PSMB3, UBC7, PSMD14, Brca1/Bard1, RING-box protein 1, PSMB7, PSMD12, PSMA3, PSMC5, BAG-1, PSMA5, HSP70, p47, Bard1, PSMA6, PSMA2, PSMD6, PSMC1, MMS2
10	Cytoskeleton spindle microtubules	0.00008172060696576	Tubulin beta, Tubulin gamma, KIF4A, HZwint-1, Cyclin B, HOOK1, Cyclin B2, ZW10, Nek2A, Tubulin alpha 1A, CENP-A, Tubulin delta, MAD2a, CENP-H, Importin (karyopherin)-alpha, Rod, RCC1, MKLP2, Kid, BUB1, Sororin, Aurora-A, Securin, CDK1 (p34), ANAPC7, Tubulin alpha, Dynein 1, cytoplasmic, heavy chain, Karyopherin alpha 2, 4.1N, DLC1 (Dynein LC8a), BUBR1, DORFIN, DEEPEST, MID1, EML4, HEC, TTK, MCAK, Cyclin B1, PAFAH alpha (LIS1), RAE1, Zwilch, Tubulin (in microtubules)