TABLE 2.

Pathway enrichment analysis in SKBR3 cells treated with ATRA

We performed enrichment analysis of the genes regulated by ATRA using Metacore-annotated pathway maps (see the Thomson Reuters Web site). Each pathway map represents a multistep canonical pathway backed by “small experiment” evidence in the literature. The pathways of particular relevance for our study are indicated in boldface type. FDR, false discovery rate.

No.	Pathway maps	Total genes	ATRA-modulated	p	FDR
1	Cell adhesion_Chemokines and adhesion	100	52	9.44E − 15	8.17E − 12
2	Cytoskeleton remodeling_TGF, WNT and cytoskeletal remodeling	111	54	1.07E − 13	4.64E − 11
3	Cytoskeleton remodeling_Cytoskeleton remodeling	102	49	2.72E − 12	7.83E − 10
4	Ligand-independent activation of androgen receptor in prostate cancer	67	35	1.93E − 10	4.18E − 08
5	Development_EGFR signaling pathway	71	36	3.19E − 10	5.52E − 08
6	Signal transduction_PKA signaling	51	29	4.89E − 10	6.59E − 08
7	Immune response_HSP60 and HSP70/TLR signaling pathway	54	30	5.33E − 10	6.59E − 08
8	Signal transduction_PTEN pathway	46	27	7.32E − 10	7.92E − 08
9	Aberrant B-Raf signaling in melanoma progression	55	30	9.73E − 10	9.35E − 08
10	Immune response_HMGB1/RAGE signaling pathway	53	29	1.68E − 09	1.45E − 07
11	Apoptosis and survival_BAD phosphorylation	42	25	2.09E − 09	1.64E − 07
12	DNA damage_ATM/ATR regulation of G1/S checkpoint	32	21	3.3E − 09	2.33E − 07
13	Signal transduction_AKT signaling	43	25	4.14E − 09	2.33E − 07
14	Apoptosis and survival_TNFR1 signaling pathway	43	25	4.14E − 09	2.33E − 07
15	Immune response_MIF-induced cell adhesion, migration and angiogenesis	46	26	4.65E − 09	2.33E − 07
16	Development_TGF-β-dependent induction of EMT via RhoA, PI3K, and ILK	46	26	4.65E − 09	2.33E − 07
17	Ovarian cancer (main signaling cascades)	64	32	4.84E − 09	2.33E − 07
18	Development_Regulation of epithelial-to-mesenchymal transition (EMT)	64	32	4.84E − 09	2.33E − 07
19	LRRK2 in neurons in Parkinson disease	33	21	7.54E − 09	3.43E − 07
20	Development_Gastrin in cell growth and proliferation	62	31	8.42E − 09	3.53E − 07
21	Development_PIP3 signaling in cardiac myocytes	47	26	8.63E − 09	3.53E − 07
22	Cell cycle_Chromosome condensation in prometaphase	21	16	8.97E − 09	3.53E − 07
23	IGF family signaling in colorectal cancer	60	30	1.46E − 08	5.51E − 07
24	Development_Cytokine-mediated regulation of megakaryopoiesis	57	29	1.54E − 08	5.54E − 07
25	Development_Prolactin receptor signaling	58	29	2.55E − 08	8.53E − 07