CCLEfullyIntercepted_EXP_CNV_miRNA_DataSET
Description
The CCLE data was obtained from https://depmap.org/portal/download/. This includes the CCLE expression data. We obtained the RNAseq TPM gene expression data for protein coding genes, also Log2 transformed with a pseudocount of 1 and the HGNC and Entrez ID identifiers (“DepMap, Broad (2021): DepMap 21Q3 Public. figshare. Dataset,” n.d.). The miRNA expression data was also obtained from Depmap (Cancer Cell Line Encyclopedia Consortium, 2015; J et al., 2012). We also obtained the CCLE ABSOLUTE copy number analysis results of 2019 (G. M et al., 2019) and mapped the CNV data of the corresponding miRNAs to the raw segmented copy-number profiles in the .seg file format (hg19) of CCLE DNA Copy Number using the GRCh38.87 version of the genome. A full interception of all datasets was performed to have a complete dataset for 904 cell lines and 18431 instances including 541 miRNAs. For a full description check our publication here: https://www.sciencedirect.com/science/article/pii/S258900422101378X The data set is formated to be used by BioNetUCR, available here: bionet.prislab.org/download DepMap, Broad (2021): DepMap 21Q3 Public. figshare. Dataset. (n.d.). Retrieved September 2, 2021, from https://figshare.com/articles/dataset/DepMap_21Q3_Public/15160110/2?file=29124102 Cancer Cell Line Encyclopedia Consortium, and G. of D. S. in C. C. (2015). Pharmacogenomic agreement between two cancer cell line data sets. Nature, 528(7580), 84–87. https://doi.org/10.1038/NATURE15736 M, G., FW, H., J, J.-V., GV, K., CC, L., ER, M., … WR, S. (2019). Next-generation characterization of the Cancer Cell Line Encyclopedia. Nature, 569(7757), 503–508. https://doi.org/10.1038/S41586-019-1186-3