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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]
  1. All the modules extracted from gene expression profiling data and used in the study. MEF, mouse embryonic fibroblast; WT, wild type.