Description Usage Source References Examples
Supervised signatures from MSigDB and derived from unsupervised classifiers. They consist of vectors for each signature giving sets of genes that are high- or down-regulated.
1 | data("supervised_signatures")
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Molecular Signature Database (MSigDB) (Subramanian, Tamayo, et al. (2005), PNAS 102, 15545-15550, http://www.broad.mit.edu/gsea/)
Boyault, S., Rickman, D.S., de Reynies, A., Balabaud, C., Rebouissou, S., Jeannot, E., Herault, A., Saric, J., Belghiti, J., Franco, D., et al. (2007). Transcriptome classification of HCC is related to gene alterations and to new therapeutic targets. Hepatol. Baltim. Md 45, 42-52.
Chiang, D.Y., Villanueva, A., Hoshida, Y., Peix, J., Newell, P., Minguez, B., LeBlanc, A.C., Donovan, D.J., Thung, S.N., Sole, M., et al. (2008). Focal gains of VEGFA and molecular classification of hepatocellular carcinoma. Cancer Res. 68, 6779-6788.
Lee, J.-S., Chu, I.-S., Heo, J., Calvisi, D.F., Sun, Z., Roskams, T., Durnez, A., Demetris, A.J., and Thorgeirsson, S.S. (2004). Classification and prediction of survival in hepatocellular carcinoma by gene expression profiling. Hepatol. Baltim. Md 40, 667-676.
Subramanian, A., Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., Gillette, M.A., Paulovich, A., Pomeroy, S.L., Golub, T.R., Lander, E.S., et al. (2005). Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. U. S. A. 102, 15545-15550.
Boyault, S., Rickman, D.S., de Reynies, A., Balabaud, C., Rebouissou, S., Jeannot, E., Herault, A., Saric, J., Belghiti, J., Franco, D., et al. (2007). Transcriptome classification of HCC is related to gene alterations and to new therapeutic targets. Hepatol. Baltim. Md 45, 42-52.
Chiang, D.Y., Villanueva, A., Hoshida, Y., Peix, J., Newell, P., Minguez, B., LeBlanc, A.C., Donovan, D.J., Thung, S.N., Sole, M., et al. (2008). Focal gains of VEGFA and molecular classification of hepatocellular carcinoma. Cancer Res. 68, 6779-6788.
Lee, J.-S., Chu, I.-S., Heo, J., Calvisi, D.F., Sun, Z., Roskams, T., Durnez, A., Demetris, A.J., and Thorgeirsson, S.S. (2004). Classification and prediction of survival in hepatocellular carcinoma by gene expression profiling. Hepatol. Baltim. Md 40, 667-676.
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