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BMC Med Genomics. 2018 Apr 20;11(Suppl 2):25. doi: 10.1186/s12920-018-0348-8.

CAS-viewer: web-based tool for splicing-guided integrative analysis of multi-omics cancer data.

Author information

1
Department of Biomedical Informatics, University of Utah, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA.
2
University of Utah, School of Computing, University of Utah, Salt Lake City, UT, 84108, USA.
3
Department of Biomedical & Translational Informatics, Geisinger Health System, Danville, PA, 17822, USA.
4
The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16082, USA.
5
Department of Biomedical Informatics, University of Utah, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA. younghee.lee@utah.edu.

Abstract

BACKGROUND:

The 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.

RESULTS:

We 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.

CONCLUSIONS:

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.

KEYWORDS:

Alternative splicing; Cancer; Genomics; Methylation; SNP; mRNA regulation; miRNA

PMID:
29697367
PMCID:
PMC5918456
DOI:
10.1186/s12920-018-0348-8
[Indexed for MEDLINE]
Free PMC Article

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