TCGASpliceSeq a compendium of alternative mRNA splicing in cancer

Area of Science:

• Genomics and Bioinformatics
• Cancer Transcriptomics
• Molecular Biology

Background:

• The Cancer Genome Atlas (TCGA) provides extensive RNASeq data for cancer transcriptomes.
• Alternative mRNA splicing is crucial in cancer development, including carcinogenesis, de-differentiation, and metastasis.
• Understanding splicing alterations is vital for cancer research.

Purpose of the Study:

• To develop TCGA SpliceSeq, a web-based resource for exploring alternative splicing patterns in TCGA tumors.
• To provide a user-friendly, visual interface for analyzing splicing data.
• To enable investigation of splicing variations between tumor types and between tumors and adjacent normal tissues.

Main Methods:

• Utilized TCGA RNASeq data for 33 different tumor types.
• Developed the SpliceSeq computational package and a web-based interface.
• Loaded Percent Spliced In (PSI) values for splice events and associated statistical summaries.

Main Results:

• TCGA SpliceSeq offers a highly visual and intuitive interface for exploring splicing patterns.
• Users can interrogate specific genes, identify genes with significant splicing variation, or compare tumor vs. normal samples.
• Splicing data, including PSI values and graphical representations, are accessible and downloadable.

Conclusions:

• TCGA SpliceSeq is a valuable, freely accessible resource for the cancer research community.
• Facilitates in-depth analysis of alternative splicing in cancer using TCGA data.
• Supports integrative analyses and discovery of novel splicing-related cancer mechanisms.