ExSurv: A web resource for prognostic analyses of exons across human cancers using clinical transcriptomes

ExSurv is a web resource for studying the survival contributions of exons across human cancers using RNA-seq data. ExSurv is the first web server which provides exon level survival significance by using the RNA-seq expression datasets and the clinical metadata for four cancer types from The Cancer Genome Atlas (TCGA) project. We pre-calculated the prognostic significance of more than 600000 annotated exons in Ensembl using survival package in R. We stored the TCGA clinical data, exon survival p-values and the expression of the significant exons for visualizing the survival curves in a MySQL database. We developed an integrated backend using PHP and R and used JavaScript in the frontend. The PHP/R backend is reponsible for querying the MySQL database upon user input, calling R to visualize the corresponding database results (using survival package) and returning these results to the frontend. In the frontend, the results are shown to the users in an organized way as a table where each row corresponds to an exon in the queried gene symbol or Ensembl gene ID. It is possible to export the survival plots in SVG (scalable vector graphics) format and the raw data used to generate the plot in TSV (tab-separated values) format.

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Posted in Softwares


School of Informatics and Computing
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email: jangalab@iupui.edu
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