MS.liverK-package: Subtyping of Liver Cancer Samples According to Various...

Description Author(s) References


Functions that return the molecular subtype of liver cancer samples according to several classifications. It reads genes expression data and runs classifiers to return the subtype described by several studies in liver cancer. This is a contribution from the Tumor Identity Cards (CIT) program founded by the Ligue Nationale Contre le Cancer (France).


Aurelien de Reynies, Florent Petitprez

Maintainer: Florent Petitprez <>


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.

Hoshida, Y., Nijman, S.M.B., Kobayashi, M., Chan, J.A., Brunet, J.-P., Chiang, D.Y., Villanueva, A., Newell, P., Ikeda, K., Hashimoto, M., et al. (2009). Integrative transcriptome analysis reveals common molecular subclasses of human hepatocellular carcinoma. Cancer Res. 69, 7385-7392.

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.

Nault, J.C., and Zucman Rossi, J. (2013). Molecular classification of hepatocellular adenomas. Int. J. Hepatol. 2013, 315947.

Roessler, S., Jia, H.-L., Budhu, A., Forgues, M., Ye, Q.-H., Lee, J.-S., Thorgeirsson, S.S., Sun, Z., Tang, Z.-Y., Qin, L.-X., et al. (2010). A unique metastasis gene signature enables prediction of tumor relapse in early-stage hepatocellular carcinoma patients. Cancer Res. 70, 10202-10212.

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.

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