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 .

中文翻译：

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Cancer DEIso：用于研究差异表达基因水平和亚型水平人类癌症标志物的综合分析平台


受选择性剪接调节的转录亚型可以极大地影响癌发生，因此需要在癌症研究中获得基因差异表达和亚型分布故障的线索。癌症基因组图谱（TCGA）项目于2008年启动，旨在从人群中收集与癌症相关的基因组突变原始数据。虽然许多存储库试图在 TCGA 中添加对原始数据的洞察，但现有的数据库还没有提供全面的基因水平和异构体水平的癌症分期标志物研究和生存分析。我们构建了 Cancer DEIso，以促进基因水平和亚型水平人类癌症研究的深入分析。在 Cancer DEIso 中收集和处理患者 RNA-seq 数据、样本表、患者临床数据和人类基因组数据集。并实现了四个搜索癌症阶段之间差异表达基因/亚型的功能：（i）搜索特定癌症类型及其两个阶段的潜在基因/亚型标记； (ii) 搜索基因/亚型的潜在诱发癌症类型和阶段； (iii) 对某些癌症的给定基因/亚型的表达存活分析； (iv) 基因/亚型阶段表达比较可视化。作为一个例子，我们证明癌症 DEIso 可以指示潜在的结直肠癌亚型诊断标志物，当仅考虑基因水平表达时，这些标志物不容易检测到。癌症 DEIso 可在 获取。