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Lina M. Gallego-Paez, Jan Mauer (BioMed X Institute, Im Neuenheimer Feld 583, 69120 Heidelberg, Germany)
Splicing of mRNA is a crucial process in eukaryotic gene expression regulation. In addition to canonical splicing, which leads to the inclusion of constitutive exons into the mature mRNA, the transcriptome is subject to alternative splicing. Alternative splicing can give rise to multiple protein-coding isoforms from a single pre-mRNA and is a major determinant for proteome diversity. Emerging data indicate that alternative splicing plays a critical role in the pathogenesis of several molecular subtypes of cancer. Interrogating such splicing abnormalities can facilitate identification of oncogenes, tumor suppressors, or drug resistance mechanisms. We have developed a computational workflow for the identification of differentially spliced regions in mRNAs across tumor types and integrated this information into a versatile database of cancer-specific splicing profiles and their association to molecular and clinical traits from tumor samples and cancer cell lines (DJEC DB). This database can be accessed through an interactive web application, which incorporates visualization of splice junction usage, junction/trait associations and junction co-expression networks.