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Table 4 Significant genes in AP-ISA biclusters and the most distinct gene enrichment pathways by Gene Ontology and KEGG

From: Analysis of breast cancer subtypes by AP-ISA biclustering

Class type Term (Enrichiment type) P-value significant genes
Normal-like regulation of cell proliferation (Gene Ontology) 4.38E-10 CDKN1C;TXNIP;DPT;EDNRB; KL;
FIGF;ANXA1;NRG1;HOXA5; ID4;
ID4;IGF1;IGFBP6;AQP1;KIT;AQP1;
LIFR;PPARG;PRNP;NDRG2; CAV1
PTN;PTPRM;RBP4;CX3CL1; CAV2;
SFRP1;TGFBR2;TGFBR3; KLF4;
KRT5;PPAP2B;KRT17;CD36; RBP4;
regulation of multicellular organismal process (Gene Ontology) 1.03E-09
cell differentiation (Gene Ontology) 1.07E-08
PPAR signaling pathway (KEGG Pathways) 4.58E-04
HER2+ single-organism process 1.29E-04 ERBB2;FGFR4;GRB7;GSK3B; FA2H;
PSMD3;BIK;CDC6;CLTC;GSK3B;
ODF2;RAP1GAP;S100A8;SDC1;CDC6;
STX1A;TMSB10;SNF8;FHOD1;
EAF2;VPS37B;WIPF2;TCAP;STARD3;
epidermal growth factor receptor signaling pathway (Gene Ontology) 6.944E-03
ERBB signaling pathway (Gene Ontology) 7.514E-03
Basal-like cell cycle process 1.09E-05 CDK6;CDKN2A;MSH2;FZD9; FABP7;
LY6D;BCL11A;CCNE1;CDC20; MIA;
CDK6;CDKN2A;CENPA;FANCA;
FOXC1;STMN1;MSH2;TTK;EN1;
CDK2AP1;RAD54L;CDC123;DSC2;
GTPBP4;PHGDH;CDCA8;B3GNT5;
CENPN;TTYH1;SUV39H2;ROPN1;
CRABP1;KLK6; VGLL1;SERPINB5;
lymphocyte differentiation (Gene Ontology) 1.019E-03
B cell activation (Gene Ontology) 8.673E-03
p53 signaling pathway (KEGG Pathways) 3.15E-04
Pathways in cancer (KEGG Pathways) 4.489E-03
Luminal-5 mammary gland epithelium development 1.15E-05 CCND1;ESR1;GATA3;TBX3; BTF3;
WNT3;BCL2;CELSR2;TLE3;CGA;
RNF43;PVALB;CPB1;SLC1A2; SKP1A;
C5orf30;SLC16A6;BEX1;GLDC;HAGH;
ZNF24;LRBA;C6orf211;YPEL3;COX6C;
LAMA3;MKL2;RAD17;BCAS1; CGN;
SERPINA5;HSPB8;COX17;ING2;
Wnt signaling pathway (Gene Ontology) 7.896E-03
CD8-positive, alpha-beta T cell lineage commitmen (Gene Ontology) 4.294E-03
Luminal-6 Glutamate receptor signaling pathway (Gene Ontology) 2.316E-03 BCL2;WNT3;ESR1;SERP1;PIGT; TLE3;STC1;ARNT2;PKIB;ZFX; HAGH;
IGBP1;HPN;DNAJC12;TBCA;BCAS1;
CCNH;ACBD4;GRIA2;CYP2A7;BAI2; GRIA1;XBP1;SIAH2;CPEB4; MAP2K4;
SLC27A2;PNPLA4;SLC1A2; MAST4;
CYB5R1;CARTPT;RABEP1;RAD17;
COX6C;QDPR;SEC11C;
CD8-positive, alpha-beta T cell lineage commitment (Gene Ontology) 3.87E-03
response to insulin-like growth factor stimulus (Gene Ontology) 7.726E-03
Retinol metabolism (KEGG Pathways) 4.07E-03
Luminal-9 CD8-positive, alpha-beta T cell lineage commitment (Gene Ontology) 4.717E-03 XBP1;BCL2;C3orf18;CIRBP;GAD1;
PKIB;APH1B;NAT1;RAB30; ABAT;
BCL2;MYO5C;CA12;SIAH2;MKL2;
TTC12;REPS2;NPY1R;KIAA1370;
NAT2;RALGPS2;CYBRD1;MUC1;
RAB31;RLN2;NTN4;MAP2K4;
MAST4;GALNT10;MYB;ESR1;
SREBF1;GFALS;TLE3;XBP1;
ACBD4;STC2;ABAT;
response to insulin-like growth factor stimulus (Gene Ontology) 9.412E-03
beta-Alanine metabolism (KEGG Pathways) 5.476E-03