TSVdb: a web-tool for TCGA splicing variants analysis

Abstract

BackgroundCollaborative projects such as The Cancer Genome Atlas (TCGA) have generated various -omics and clinical data on cancer. Many computational tools have been developed to facilitate the study of the molecular characterization of tumors using data from the TCGA. Alternative splicing of a gene produces splicing variants, and accumulating evidence has revealed its essential role in cancer-related processes, implying the urgent need to discover tumor-specific isoforms and uncover their potential functions in tumorigenesis.ResultWe developed TSVdb, a web-based tool, to explore alternative splicing based on TCGA samples with 30 clinical variables from 33 tumors. TSVdb has an integrated and well-proportioned interface for visualization of the clinical data, gene expression, usage of exons/junctions and splicing patterns. Researchers can interpret the isoform expression variations between or across clinical subgroups and estimate the relationships between isoforms and patient prognosis. TSVdb is available at http://www.tsvdb.com, and the source code is available at https://github.com/wenjie1991/TSVdb.ConclusionTSVdb will inspire oncologists and accelerate isoform-level advances in cancer research.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4775-x) contains supplementary material, which is available to authorized users.

Identification of novel alternative splicing isoform biomarkers and their association with overall survival in colorectal cancer

“…We searched all the 9 genes identified in this study (CLK1, COL6A3, CD44, ARHGEF9, HKDC1, CHEK1, HNF4A, SERPINA1, CALD1) against TSVdb and downloaded the junction usage value for colon adenocarcinoma (COAD) and rectum adenocarcinoma (READ). Junction usage is calculated by dividing junction quantification value to mean junction quantification value of that person for a specific gene [39]. We combined junction usage for 379 primary solid tumor samples with 1 , consistent with what we observed in the two GEO datasets.…”

Identification of novel alternative splicing isoform biomarkers and their association with overall survival in colorectal cancer

“…All patient overall survival (OS) data and junction usage data were downloaded from TSVdb [27]. All patients with OS data were separated into two groups based on the median value of a particular junction usage.…”

“…To validate the splicing events identified in this study in an independent dataset, we used a recently developed tool TSVdb [27], which integrates and visualizes alternative splicing data based on TCGA samples for 33 tumor types. We searched all the 10 genes identified in this study (CLK1, COL6A3, CD44, ARHGEF9, HKDC1, CHEK1, HNF4A, SERPINA1, CALD1, FBLN2) against TSVdb and downloaded the junction usage value for colon adenocarcinoma (COAD) and rectum adenocarcinoma (READ).…”

“…We searched all the 10 genes identified in this study (CLK1, COL6A3, CD44, ARHGEF9, HKDC1, CHEK1, HNF4A, SERPINA1, CALD1, FBLN2) against TSVdb and downloaded the junction usage value for colon adenocarcinoma (COAD) and rectum adenocarcinoma (READ). Junction usage is calculated by dividing junction quantification value to mean junction quantification value of that person for a specific gene [27]. We combined junction usage for 379 primary solid tumor samples with 1 metastatic and 2 recurrent solid tumor samples and compared with 51 normal colon or rectal tissue samples.…”

MetaMap, an interactive webtool for the exploration of metatranscriptomic reads in human disease-related RNA-seq data

“…Due to both volume and complexity of the data as well as availability only in matrix 45 form, users without bioinformatic expertise may find it challenging to explore this resource. A number of previous studies have shown that interactive webtools enable easy exploration of large and complex molecular data sets (Sun et al, 2018;Dumas et al, 2016;Ono et al, 2017). Therefore, we developed the user-friendly, interactive MetaMap webtool.…”