TABLE 3.

Process/network enrichment analysis in SKBR3 cells treated with ATRA

We performed enrichment analysis of the genes regulated by ATRA using Metacore-annotated process networks (see the Thomson Reuters Web site). The content of these cellular and molecular processes is defined and annotated by Thomson Reuters scientists. Each process represents a preset network of protein interactions characteristic for the process. The processes of particular relevance for our study are indicated in boldface type.

No.	Process networks	Total genes	ATRA-modulated	p	FDR
1	Development_EMT_Regulation of epithelial-to-mesenchymal transition	225	104	2.2426E − 10	3.5657E − 08
2	Cell cycle_G1-S growth factor regulation	195	92	6.7242E − 10	5.3457E − 08
3	Cell cycle_G2-M	206	95	1.6024E − 09	8.4929E − 08
4	Signal transduction_WNT signaling	177	83	6.6881E − 09	2.6585E − 07
5	Cell cycle_Mitosis	179	83	1.2834E − 08	4.0814E − 07
6	Reproduction_Progesterone signaling	214	93	8.7775E − 08	2.326E − 06
7	Cell cycle_G1-S interleukin regulation	128	62	1.2866E − 07	2.9225E − 06
8	Development_Hemopoiesis, erythropoietin pathway	136	64	3.085E − 07	5.9313E − 06
9	Development_Blood vessel morphogenesis	228	96	3.3573E − 07	5.9313E − 06
10	Apoptosis_Anti-apoptosis mediated by external signals via MAPK and JAK/STAT	179	79	3.8476E − 07	6.1177E − 06
11	Inflammation_TREM1 signaling	145	66	9.1905E − 07	1.3285E − 05
12	Inflammation_Amphoterin signaling	118	55	3.0139E − 06	3.9935E − 05
13	Inflammation_IL-6 signaling	119	55	4.1577E − 06	5.0852E − 05
14	Development_Hedgehog signaling	254	100	7.394E − 06	8.3975E − 05
15	Cytoskeleton_Actin filaments	176	74	7.9534E − 06	8.4306E − 05
16	Cell adhesion_Integrin-mediated cell-matrix adhesion	214	86	1.283E − 05	0.00012069
17	Reproduction_Feeding and neurohormone signaling	211	85	1.2904E − 05	0.00012069
18	Cell cycle_S phase	149	64	1.4311E − 05	0.00012216
19	Cytoskeleton_Spindle microtubules	109	50	1.4597E − 05	0.00012216
20	Inflammation_IL-2 signaling	104	48	1.7613E − 05	0.00014002
21	Apoptosis_Anti-apoptosis mediated by external signals via NF-κB	111	50	2.6843E − 05	0.00019491
22	Signal transduction_NOTCH signaling	236	92	2.6969E − 05	0.00019491
23	Inflammation_IFN-γ signaling	110	49	4.6056E − 05	0.00031838
24	Signal Transduction_TGF-β, GDF and activin signaling	154	64	4.9437E − 05	0.00031887
25	Cell adhesion_Attractive and repulsive receptors	175	71	5.0136E − 05	0.00031887