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

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