Bioinformatics & Systems Biology

Biography

Biography: Mader Sylvie

Abstract

MiSTIC is a unique software package designed to visualize and annotate gene-gene correlations at different resolution levels, from global transcriptomes to gene correlation clusters to individual genes. MiSTIC compares correlation structures of large transcriptome datasets, revealing similitudes between datasets from different solid tumor types, in keeping with common gene reprogramming events in these cancers. Within datasets, MiSTIC performs systematic enrichment analysis on correlated gene clusters to explore their biological significance, using gene sets from multiple databases and lists of genes containing transcription factor binding sites or ChIP-Seq regions in their flanking sequences. This enables the rapid identification of potential causes of gene clustering, including gene amplification/deletion or transcription networks. Enrichment analysis performed at the dataset level can also directly visualize the main aspects of tumor heterogeneity targeted by each gene signature in the database, illustrating for instance that all breast cancer prognostic signatures as well as subtype classifiers are enriched in a proliferation cluster highly conserved among different cancers. Finally, patient sets defined by expression of selected biomarker genes can be visualized, compared and annotated for enrichment in clinical features. Examples will be provided to illustrate how MiSTIC greatly facilitate both the mechanistic exploration of cancer biology and tumor classification using public or in-house transcriptome datasets. A version of MiSTIC pre-loaded with public tumor transcriptome datasets and relevant gene signatures will be made accessible via web interface, and the software package will be distributed for analysis of custom datasets.