laml {iClusterVB}

LAML (Acute Myeloid Leukemia) Data

Description

This is a subset of the LAML (Acute Myeloid Leukemia) data (TCGA, 2013). The Acute Myeloid Leukemia (laml_tcga) datasets were download using the cBioPortal for Cancer Genomics tool (Cerami et al., 2012; Gao et al., 2013). The 170 samples with gene expression data and mutation data were included. Only a subset of the genes was selected, as desribed below. To access the data containing all the genes, please visit: https://github.com/AbdalkarimA/iClusterVB

Usage

data(laml)

Value

Within the data file, there is:

laml.cli:

A dataframe of clinical information for the 170 samples.

laml.exp:

A matrix of 170 samples and the gene expression values of the 500 genes chosen by Zainul Abidin and Westhead (2016) based on having the highest ranked-based coefficients of variation and standard deviation across the samples. Some names may have been updated or corrected from the supplementary material.

laml.mut:

A matrix of 170 samples and the mutation status of 156 genes that had >=2 mutations. 1 indicates the presence of mutation, and 0 indicates the absence of mutation.

References

Cancer Genome Atlas Research Network, Ley, T. J., Miller, C., Ding, L., Raphael, B. J., Mungall, A. J., Robertson, A., Hoadley, K., Triche, T. J., Jr, Laird, P. W., Baty, J. D., Fulton, L. L., Fulton, R., Heath, S. E., Kalicki-Veizer, J., Kandoth, C., Klco, J. M., Koboldt, D. C., Kanchi, K. L., Kulkarni, S., … Eley, G. (2013). Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. The New England journal of medicine, 368(22), 2059–2074. https://doi.org/10.1056/NEJMoa1301689

Cerami, E., Gao, J., Dogrusoz, U., Gross, B. E., Sumer, S. O., Aksoy, B. A., Jacobsen, A., Byrne, C. J., Heuer, M. L., Larsson, E., Antipin, Y., Reva, B., Goldberg, A. P., Sander, C., & Schultz, N. (2012). The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer discovery, 2(5), 401–404. https://doi.org/10.1158/2159-8290.CD-12-0095

Gao, J., Aksoy, B. A., Dogrusoz, U., Dresdner, G., Gross, B., Sumer, S. O., Sun, Y., Jacobsen, A., Sinha, R., Larsson, E., Cerami, E., Sander, C., & Schultz, N. (2013). Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Science signaling, 6(269), pl1. https://doi.org/10.1126/scisignal.2004088

Zainul Abidin, F. N., & Westhead, D. R. (2017). Flexible model-based clustering of mixed binary and continuous data: application to genetic regulation and cancer. Nucleic acids research, 45(7), e53. https://doi.org/10.1093/nar/gkw1270