Table 1. Gene Set Enrichment Analysis (GSEA) of EpFra1 cells.
|
a. Upregulated set | ||
|---|---|---|
| No. of genes in comparison (n): 381 | ||
| Collection | Description | P-value |
| CP: canonical pathways | Genes involved in interleukin-6 signalling | 5.58 e−5 |
| Genes involved in extracellular matrix organization | 8.69 e−5 | |
| IL-6 signalling pathway | 2.65 e−4 | |
| Osteopontin-mediated events | 2.92 e−4 | |
| Toll-like receptor signalling pathway | 4.41 e−4 | |
| HIF-1-alpha transcription factor network | 5.04 e−4 | |
| AP-1 transcription factor network | 8.12 e−4 | |
| IL-6-mediated signalling events | 8.30 e−4 | |
| ATF-2 transcription factor network | 9.09 e−4 | |
| Validated transcriptional targets of AP1 family members Fra1 and Fra2 | 9.13 e−4 | |
| Genes involved in degradation of the extracellular matrix | 1.30 e−3 | |
| CGP: chemical and genetic perturbations | The 'adult tissue stem' module: genes coordinately upregulated in a compendium of adult tissue stem cells | < 1 e−16 |
| Genes upregulated in invasive ductal carcinoma (IDC) relative to ductal carcinoma in situ (DCIS, non-invasive). | <1 e−16 | |
| Genes upregulated during epithelial-to-mesenchymal transition (EMT) induced by TGFB1 in the EpH4 cells transformed by HRAS) | <1 e−16 | |
| Upregulated genes in the cancer gene signature, representing a gene signature of cellular transformation | 2.22 e−16 | |
| Genes downregulated in MCF7 cells at 24 h of estradiol treatment | 3.33 e−16 | |
| Genes upregulated in MCF7 cells under hypoxia conditions | 1.28 e−14 | |
| Genes upregulated upon overexpression of PARVB in MDA-MB-231 cells cultured in 3D Matrigel only | 4.57 e−14 | |
| Genes downregulated in luminal-like breast cancer cell lines compared with the mesenchymal-like ones | 6.91 e−14 | |
| Genes upregulated in MCF7 cells treated with hypoxia mimetic DMOG | 3.65 e−13 | |
| Genes downregulated in luminal-like breast cancer cell lines compared with the basal-like ones | 5.90 e−12 | |
| Genes upregulated in response to both hypoxia and overexpression of an active form of HIF1A | 6.79 e−12 | |
| |
Genes consistently upregulated in mammary stem cells both in mouse and human species |
9.59 e−12 |
|
b. Downregulated set | ||
| No. of genes in comparison (n): 246 | ||
|
Collection |
Description |
P-value |
| CP: canonical pathways | Genes involved in cell–cell junction organization | 8.95 e−4 |
| Genes involved in tight junction interactions | 1.13 e−3 | |
| Genes involved in cell junction organization | 1.46 e-−3 | |
| Genes involved in apoptotic cleavage of cell adhesion proteins | 3.96 e−3 | |
| Genes involved in cell–cell communication | 6.45 e−3 | |
| CGP: chemical and genetic perturbations | Genes consistently downregulated in mammary stem cells both in mouse and human species | < 1 e−13 |
| Genes downregulated in HMLE cells after E-cadhedrin knockdown by RNAi | < 1 e−13 | |
| Genes upregulated in luminal-like breast cancer cell lines compared with the mesenchymal-like ones | 1.70 e−13 | |
| Genes upregulated in MDA-MB-231 cells after knockdown of ZEB1 by RNAi | 1.96 e−13 | |
| Genes upregulated in basal-like breast cancer cell lines as compared with the mesenchymal-like ones | 1.28 e−12 | |
| Myb-regulated genes in MCF7 and lung epithelial cell lines overexpressing MYBL2, MYBL1 or MYB | 6.08 e−12 | |
| Genes associated with a migration rate of 40 human bladder cancer cells | 9.03 e−12 | |
| Genes with promoters occupied by SMAD2 or SMAD3 in HaCaT cells (keratinocyte) according to a ChIP-chip analysis | 7.43 e−11 | |
Comparative analysis of the gene sets upregulated (a) or downregulated (b) in EpFra1 cells compared with EpH4 cells with the Molecular Signatures Database. The most significant overlaps with curated expression signatures from the CGP (with focus on mammary-related signatures) and the CP collections are presented, relevant keywords highlighted in bold, and the P-values are indicated