CELLector.CellLine.BEMs_v2: Cell Lines' Binary Genomic/Epigenomic Event Matrices

In najha/CELLector: Genomics guided selection of cancer cell lines

Cell Lines' Binary Genomic/Epigenomic Event Matrices

Description

A list containing 16 data frames (one for cancer type), identified through TCGA labels. Each of these data frames contains cell lines' binary event matrices (BEMs) with the status (presence/absence) of cancer functional events (CFEs, somatic mutations in high-confidence cancer driver genes, copy number altered genomic segments and hypermethylated gene promoters) as defined in [1].

Usage

data("CELLector.CellLine.BEMs_v2")

Format

A named list of data frames (with TCGA cancer type labels as names). Each of these data frames contains two columns with COSMIC [2] identiefiers and names of cell lines (one per row), respectively, and then binary entries indicating the status of each CFEs (one per column) across cell lines.

Details

BEMs for cell lines from the Genomics of Drug Sensitivity in Cancer (GDSC1000, [1]) panel. Data is available for cell lines matching one among 16 different TCGA cancer types: BLCA, BRCA, COREAD, GBM, HNSC, KIRC, LAML, LGG, LUAD, LUSC, OV, PRAD, SKCM, STAD, THCA, UCEC.

A decoding table for these labels is available at

https://www.cancerrxgene.org/gdsc1000/GDSC1000_WebResources/Data_Summary.html.

Each data frame contains cell lines on the rows (with COSMIC identifiers and names, respectively on first and second column) and then a binary matrix with a CFE per column and entries indicating the presence/absence of a given CFE in a given cell line.

Gene symbols as row names indicate high confidence cancer driver genes and the entries in the corresponding rows indicate the presence/absence of somatic mutations. Row names with cna as prefix indicates chromosomal segments that are recurrently copy number altered in cancer (RACSs, defined in [1]), hms as a prefix indicates hypermethylated gene promoters (HMS, defined in [1]). A list with all the considered CFEs is available in the CELLector.CFEsV2 data object. A decoding table for the RACSs is available in the CELLector.CFEs.CNAid_decode object, with the mapping realised by the values in the CNA_identifier column. A decoding table for the HMS is available in the CELLector.CFEs.HMSid_decode object, with the mapping realised by the values in the hms_id column.

Please note that the same RACS identifier across multiple cancer types might indicate different chromosomal regions, therefore in order to be decode it should be considered jointly with the TCGA label of the data frame it has been extracted from.

Author(s)

Francesco Iorio ([e-mail])

References

[1] Iorio, F. et al. A Landscape of Pharmacogenomic Interactions in Cancer. Cell 166, 740–754 (2016).

[2] Forbes, S. A. et al. COSMIC: exploring the world’s knowledge of somatic mutations in human cancer. Nucleic Acids Res. 43, D805–11 (2015).

See Also

CELLector.CellLine.BEMs, CELLector.PrimTum.BEMs_v2, CELLector.CFEsV2, CELLector.CFEs.CNAid_decode, CELLector.CFEs.HMSid_decode

Examples

data(CELLector.CellLine.BEMs)
CELLector.CellLine.BEMs_v2$COREAD[1:10,
                               c("COSMIC_identifier","CellLine",'BRAF','hms70','cna27')]

najha/CELLector documentation built on Feb. 8, 2023, 5:35 a.m.