scan_tcga tools for integrated epigenomic and transcriptomic analysis of tumor subgroups.
The Cancer Genome Atlas contains multiple levels of genomic data (mutation, gene expression, DNA methylation, copy number variation) for 33 cancer types for almost 11,000 patients. However, a dearth of appropriate software tools makes it difficult for bench scientists to use these data effectively.



Here, we present a suite of flexible, fast and command line-based scripts that will allow retrieval and analysis of DNA methylation (tool: scan_tcga_methylation.awk), mRNA (tool: scan_tcga_mRNA.awk) and miRNA expression (tool: scan_tcga_miRNAs.awk) from cancer genome atlas network level 3 data.



We demonstrate the utility of these tools by analyzing DNA methylation and mRNA expression signatures of 60 frequently deregulated cancer genes and also of 30 miRNAs in primary (n = 102) and metastatic melanoma patients (n = 367).



Our analysis illustrates the validity of the scan_tcga tools and reveals the epigenomic signatures and importance of identifying smaller patient subgroups with distinct molecular profiles.
Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand.|Maurice Wilkins Centre for Molecular Biodiscovery, level 2, 3A Symonds Street, Auckland, New Zealand.
Aniruddha
A
Chatterjee
Department of Biochemistry, University of Otago, 710 Cumberland Street, Dunedin 9054, New Zealand.
Peter A
PA
Stockwell
Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand.|Maurice Wilkins Centre for Molecular Biodiscovery, level 2, 3A Symonds Street, Auckland, New Zealand.
Euan J
EJ
Rodger
Department of Mathematics & Statistics, University of Otago, 710 Cumberland Street, Dunedin 9054, New Zealand.
Matthew F
MF
Parry
Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand.|Maurice Wilkins Centre for Molecular Biodiscovery, level 2, 3A Symonds Street, Auckland, New Zealand.
Michael R
MR
Eccles
D019175:DNA Methylation; D057890:Epigenomics; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008545:Melanoma / Q000235:genetics*; D035683:MicroRNAs / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics; D012878:Skin Neoplasms / Q000235:genetics*
D035683:MicroRNAs; D012333:RNA, Messenger
DNA methylation; cancer genome atlas; gene expression; melanoma; miRNA