supervised_signatures: Supervised signatures from Molecular Signature Database...

In cit-bioinfo/MS.liverK: Subtyping of Liver Cancer Samples According to Various Unsupervised or Supervised Classifiers Based on Gene Expression Data

Description

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.

Usage

data("supervised_signatures")

Source

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.

References

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.

Examples

data(supervised_signatures)

cit-bioinfo/MS.liverK documentation built on Aug. 14, 2019, 10:34 a.m.