All posts from TARGETgene

TARGETgene 2.0beta

A fusion gene that results from chromosome rearrangements is a hybrid gene formed from distinct genes, either in the same chromosome or in different chromosomes. Many recurring gene fusions, such as BCR-ABL in chronic myelogenous leukemia, EWS-FIL1 in Ewing’s Sarcoma, and TMPRSS2-ERG in prostate cancer, play important roles in cancer progression. As such, they have become important therapeutic targets. Gene fusions are currently being discovered at an increasing rate using massively parallel sequencing technologies. Prioritization of important cancer fusion drivers for validation and  as therapeutic targets cannot be performed using traditional single-gene based methods because fusions involve portions of two partner genes. To address this problem, Wu et al (Wu et al., 2013) have introduced a novel network analysis method called fusion centrality that is specifically tailored for prioritizing gene fusions. This fusion centrality approach is now integrated into the TARGETgene software developed previously, to prioritize fusion drivers from hundreds… Read more

Release of TARGETgene

The vast array of in silico resources currently available in the life sciences research offers the possibility of aiding the drug discovery process. Core Project 1 of the BMSR has developed TARGETgene to exploit these resources and to allow the identification of potential therapeutic targets and drugs in cancer using genetic network-based approaches. TARGETgene is a MATLAB tool that can rapidly extract genetic interactions from a precompiled database, allowing millions of interactions involving thousands of candidate genes to be mapped within minutes to a gene network we developed for this purpose (Wu, Asgharzadeh, Triche, D’Argenio, Bioinformatics 26:807-813, 2010). An Overview, User’s Guide and Installation details for TARGETgene are provide on this web site.  See also the following publication: Wu, D’Argenio, Asgharzadeh, Triche. PLos ONE 7:e43305, 2012.