Abstract
BackgroundThe Cancer Genome Atlas (TCGA) project is a public resource that provides transcriptomic, DNA sequence, methylation, and clinical data for 33 cancer types. Transforming the large size and high complexity of TCGA cancer genome data into integrated knowledge can be useful to promote cancer research. Alternative splicing (AS) is a key regulatory mechanism of genes in human cancer development and in the interaction with epigenetic factors. Therefore, AS-guided integration of existing TCGA data sets will make it easier to gain insight into the genetic architecture of cancer risk and related outcomes. There are already existing tools analyzing and visualizing alternative mRNA splicing patterns for large-scale RNA-seq experiments. However, these existing web-based tools are limited to the analysis of individual TCGA data sets at a time, such as only transcriptomic information.ResultsWe implemented CAS-viewer (integrative analysis of Cancer genome data based on Alternative Splicing), a web-based tool leveraging multi-cancer omics data from TCGA. It illustrates alternative mRNA splicing patterns along with methylation, miRNAs, and SNPs, and then provides an analysis tool to link differential transcript expression ratio to methylation, miRNA, and splicing regulatory elements for 33 cancer types. Moreover, one can analyze AS patterns with clinical data to identify potential transcripts associated with different survival outcome for each cancer.ConclusionsCAS-viewer is a web-based application for transcript isoform-driven integration of multi-omics data in multiple cancer types and will aid in the visualization and possible discovery of biomarkers for cancer by integrating multi-omics data from TCGA.
Highlights
The Cancer Genome Atlas (TCGA) project is a public resource that provides transcriptomic, DNA sequence, methylation, and clinical data for 33 cancer types
CAS-viewer is a web-based application for transcript isoform-driven integration of multi-omics data in multiple cancer types and will aid in the visualization and possible discovery of biomarkers for cancer by integrating multi-omics data from TCGA
MiRNA target sites: The miRNA target sites in the 3’ untranslated regions (UTRs) were compiled by integration of three miRNA target databases: 1) miRTarBase [11], which is based on experimentally validated miRNA targets; 2) TargetScan (Release 7.0) [12], which is based on conserved complementarity between targets of miRNAs and mRNAs; and 3) MicroRNA.org, which is based on the miRanda algorithm [13]
Summary
The Cancer Genome Atlas (TCGA) project is a public resource that provides transcriptomic, DNA sequence, methylation, and clinical data for 33 cancer types. There are already existing tools analyzing and visualizing alternative mRNA splicing patterns for large-scale RNA-seq experiments These existing webbased tools are limited to the analysis of individual TCGA data sets at a time, such as only transcriptomic information. Han et al BMC Medical Genomics 2018, 11(Suppl 2): and SpliceSeq [9] Most of these existing resources are available for exploring alternative mRNA splicing patterns but it is limited to transcriptome based visualization alone. MEXPRESS is a well-designed web-based tool for easy visualization and analysis of multi-layer of omics data TCGA expression, DNA methylation, and clinical data [10] but lacks the ability to explore alternative mRNA splicing patterns
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