Table 1. Biological features of selected gene co-expression modules. For DCIS, we only report observations that are replicated in the two DCIS datasets analyzed.

Module	Stage and main direction	#Genes	Top 5 hubs	Biological Function	PPI network	PPI hubs
M1-Green	Normal > DCIS > Basal	300	EBF1, AKAP12, GNG11, MRGPRF, OLFML1	Angiogenesis	57	MEOX2, CAV1, TCF4
M2-Brown	Normal > Basal	136	MLPH, ANKRD30A, FOXA1, AGR2, ERBB4	Gland development	18	SPDEF, RAB27B
M3-Darkred	Normal > (DCIS = Basal)	31	CCDC144CP, MEFV, PGM5P2, OPHN1, FRG1BP	Transport	0
M4-Turquoise	Normal < DCIS < Basal	434	CCNA2, MAD2L1, TPX2, UBE2T, CDK1	Cell cycle	324	MCM2, PCNA, AURKA, CDK1
M5-Yellow	Normal > DCIS > Basal	122	GPD1, CIDEC, PCK1, TUSC5, LEP	Lipid metabolism	13	ALDOC
M6-Purple	Normal < (DCIS = Basal)	73	CHMP2B, SMIM15, NRBF2, TMEM251, UBE2G1	Lipid metabolism	8
M7-Black	Normal < Basal	225	CD86, FYB, SAMSN1, TFEC, PTPRC	Immune response	86	ISG15, STAT1, HLA-C
M8-Darkturquoise	Normal > (DCIS = Basal)	26	STARD9, SCN3B, ACSM2A, MEG3, HDC	Respiratory chain	4
M9-Darkgrey	Normal < Basal	67	YWHAE, KLHDC3, TUBB, SLC25A39, PPP2R1A	Protein localization	29	ARRB2, YWHAE, HSP90AB1
M10-Cyan	Normal < DCIS > Basal	46	DMXL1, RNF111, ATP8B1, FAM179B, CETN3	Protein ubiquitination	0
M15-Royalblue	Normal < Basal	34	PFN1, RPS7, ERI3, TOMM20, SSB	Metabolism and RNA processing	9	RPS7