Cancer DEIso: An integrative analysis platform for investigating differentially expressed gene-level and isoform-level human cancer markers

Tzu Hsien Yang, Yu Hsuan Chiang, Sheng Cian Shiue, Po Heng Lin, Ya Chiao Yang, Kai Chi Tu, Yan Yuan Tseng, Joseph T. Tseng, Wei Sheng Wu

研究成果: Article同行評審

摘要

Transcript isoforms regulated by alternative splicing can substantially impact carcinogenesis, leading to a need to obtain clues for both gene differential expression and malfunctions of isoform distributions in cancer studies. The Cancer Genome Atlas (TCGA) project was launched in 2008 to collect cancer-related genome mutation raw data from the population. While many repositories tried to add insights into the raw data in TCGA, no existing database provides both comprehensive gene-level and isoform-level cancer stage marker investigation and survival analysis. We constructed Cancer DEIso to facilitate in-depth analyses for both gene-level and isoform-level human cancer studies. Patient RNA-seq data, sample sheets, patient clinical data, and human genome datasets were collected and processed in Cancer DEIso. And four functions to search differentially expressed genes/isoforms between cancer stages were implemented: (i) Search potential gene/isoform markers for a specified cancer type and its two stages; (ii) Search potentially induced cancer types and stages for a gene/isoform; (iii) Expression survival analysis on a given gene/isoform for some cancer; (iv) Gene/isoform stage expression comparison visualization. As an example, we demonstrate that Cancer DEIso can indicate potential colorectal cancer isoform diagnostic markers that are not easily detected when only gene-level expressions are considered. Cancer DEIso is available at http://cosbi4.ee.ncku.edu.tw/DEIso/.

原文English
頁(從 - 到)5149-5159
頁數11
期刊Computational and Structural Biotechnology Journal
19
DOIs
出版狀態Published - 2021 一月

All Science Journal Classification (ASJC) codes

  • 生物技術
  • 生物物理學
  • 結構生物學
  • 生物化學
  • 遺傳學
  • 電腦科學應用

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