Table 2 List of modules extracted from expression data
From: Sample-level enrichment analysis unravels shared stress phenotypes among multiple cancer types
Name | Description | Number of genes | Reference |
|---|---|---|---|
CIN genes | A signature of genes upregulated in chromosomal instability and predictive of clinical outcome | 70 | [35] |
Rb-E2F targets | Rb-E2F interaction network built computationally using protein interaction databases | 147 | [43] |
Down in senescence bypass | Genes downregulated in fibroblasts that bypass RAS-induced senescence | 3, 030 | [37] |
Up in senescence bypass | Genes upregulated in fibroblasts that bypass RAS-induced senescence | 2, 714 | [37] |
Down in senescence | Genes downregulated in fibroblasts in replicative senescence | 6, 122 | [42] |
Up in senescence | Genes upregulated in fibroblasts in replicative senescence | 6, 048 | [42] |
Pujana ATM network | Computational network around Atm built using expression profiling and functional and genomic data | 1, 041 | [45] |
Pujana BRCA1 network | Computational network around Brca1 built using expression profiling and functional and genomic data | 1, 198 | [45] |
Pujana BRCA2 network | Computational network around Brca2 built using expression profiling and functional and genomic data | 305 | [45] |
Pujana CHEK2 network | Computational network around Chek2 built using expression profiling and functional and genomic data | 559 | [45] |
Pujana XPRSS network | Computational network around Xprss built using expression profiling and functional and genomic data | 118 | [45] |
Bortezomib treatment DOWN | Genes downregulated in cancer cells treated with bortezomib | 1, 769 | [47] |
Bortezomib treatment UP | Genes upregulated in cancer cells treated with bortezomib | 1, 278 | [47] |
Eeyarestatin treatment DOWN | Genes downregulated in cancer cells treated with eeyarestatin | 2, 170 | [47] |
Eeyarestatin treatment UP | Genes upregulated in cancer cells treated with eeyarestatin | 2, 062 | [47] |
Downreg in PI3K-hyper | Genes downregulated in Rb-deficient breast cancer cell line treated with rapamycin | 100 | [49] |
Upreg in Pi3K-hyper | Gene upregulated in hormone therapy-resistant breast cancer | 1, 475 | [49] |
PTEN mutation signature | PTEN mutation signature upregulated in PTEN-mutant breast cancer | 592 | [50] |
Up in TSC1 mTORC1 | Genes upregulated in Tsc1-/- mutant versus WT MEFs | 167 | [51] |
Down in TSC1 mTORC1 | Genes downregulated in Tsc1-/- mutant versus WT MEFs | 101 | [51] |