Table II.

Canonical pathways enriched with differentially expressed genes.

	trMCF clone 11 vs. MCF-10F	ATRA trMCF clone 11 vs. trMCF clone 11
Aryl hydrocarbon receptor signaling	ALDH1A3↓, CCND1↓, TGFBR2↓, TGM2 ↓, TFDP1↓, ALDH3A2↑, CYP1B1↑	ALDH1A3↑, CCND1↑, TGFB2↑, TGM2↑,TFDP1↑, ALDH3A2↓, CYP1B1↓
	Other genes: CDKN1A↓, JUN↓ ALDH7A1↑, CSNK2A1↑, TGFB1↑, MAPK1↑, NFE2L2↑	Other genes: CCNE1↑, CCNE2↑, CDK6↑,DHFR↑, IL1B↑, IL6↑, NR2F1↑, NRIP1↑, POLA1↑ ALDH3B2↓, ARNT↓, NCOA3↓, HSPB2↓, ALDH6A1↓
RAR activation	ALDH1A3↓, DHRS9↓, NSD1↓, TGFB2↓, CSNK2A2↑, PIK3CD↑, PRMT2↑, PTEN↑	ALDH1A3↑, DHRS9↑, NSD1↑, TGFB2↑, CSNK2A2↓, PIK3CD↓, PRMT2↓, PTEN↓
	Other genes: JUN↓, NR2F2↓, RBP1↓, CSNK2A1↑, CSNK2A2↑, MAPK1↑, MAPK14↑, TGFB1↑, GNAS↑	Other genes: GTF2H2↑, IGFBP3↑, MAP2K1↑, MAPK13↑, NR2F1↑, NRIP1↑, RKAR2B↑, DH10↑, CITED2↓, PNRC1↓, PRKAR1A↓, SMARCD2↓
Xenobiotic metabolism signaling	ALDH1A3↓, HS3ST1↓, HS6ST2↓, PPP2R1B↓, ALDH3A2↑, CYP1B1↑, MAP2K5↑, PIK3CD↑, UGT1A1 (and others UGT)↑	ALDH1A3↑, HS3ST1↑, HS6ST2↑, PPP2R1B↑, ALDH3A2↓, CYP1B1↓, MAP2K5↓, PIK3CD↓, UGT1A1 (and others UGT)↓
	Other genes: CHST15↓, ALDH7A1↑, CAMK1D↑, HDAC4↑, MAPK1↑, MAPK14↑, MGMT↑, UGT8↑, NFE2L2↑	Other genes: ILIB↑, IL6↑, NRIP1↑, MAP2K1↑, MAPK13↑, ALDH3B2↓, ARNT↓, CAMK2D↓, CITED2↓, MAP3K8↓, PPP2R3A↓, ALDH6A1↓, MAP3K2↓
Molecular mechanisms of cancer	TGFB2↓, TGFBR2↓, CCND1↓, FZD8↓, PLCB4↓, RABIF↓, RHOF↓, GNA13↑, GNAI1↑, CD44↑	TGFB2↑, TGFBR2↑, CCND1↑, FZD8↑, PLCB4↑, RABIF↑, RHOF↑, GNA13↓, GNAI1↓, CD44↓
	Other genes: CDKN1A↓, CTNNB1↓, FYN↓, IRS1↓, JUN↓, SMAD4↓, TCF4↓, XIAP↓, PIK3CD↑, TCF3↑, TGFB1↑, GNAL↑, MAPK1↑, MAPK14↑	Other genes: APC↑, CCNE1↑, CCNE2↑, CDC25A↑, CDK6↑, CYCS↑, E2F2↑, MAP2K1↑, MAPK13↑, PRKAR2B↑, RAPGEF3↑, RBL1↑, TFDP1↑, ARHGEF10↓, FOXO1↓, HHAT↓, IRS1↓, NF1↓, PAK3↓, PIK3CD↓, PRKAR1A↓, RALGDS↓, RHOV↓

Genes downregulated (↓) or upregulated (↑) are shown. ATRA trMCF clone 11 refers to trMCF clone 11 treated with 10⁻⁶ M ATRA.