Paull EO, Carlin DE, Niepel M, Sorger PK, Haussler D, and Stuart JM (2013). Discovering Causal Pathways Linking Genomic Events to Transcriptional States Using Tied Diffusion through Interacting Events (TieDIE). Bioinformatics PMC3799471 PMID: 23986566.
Abstract
MOTIVATION: Identifying the cellular wiring that connects genomic perturbations to transcriptional changes in cancer is essential to gain a mechanistic understanding of disease initiation, progression and ultimately to predict drug response. We have developed a method called Tied Diffusion Through Interacting Events (TieDIE) that uses a network diffusion approach to connect genomic perturbations to gene expression changes characteristic of cancer subtypes. The method computes a subnetwork of protein-protein interactions, predicted transcription factor-to-target connections and curated interactions from literature that connects genomic and transcriptomic perturbations. RESULTS: Application of TieDIE to The Cancer Genome Atlas and a breast cancer cell line dataset identified key signaling pathways, with examples impinging on MYC activity. Interlinking genes are predicted to correspond to essential components of cancer signaling and may provide a mechanistic explanation of tumor character and suggest subtype-specific drug targets. AVAILABILITY: Software is available from the Stuart lab’s wiki: https://sysbiowiki.soe.ucsc.edu/tiedie. CONTACT: jstuart [at] ucsc [dot] edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.