HIT'nDRIVE is a network based cancer driver gene prioritization algorithm. It is a combinatorial optimization method that integrates genomic changes with changes in transcriptome (expression outliers) to identify a set of patient-specific, sequence-altered genes, with sufficient collective influence over dysregulated transcripts. HIT'nDRIVE aims to solve the “random walk facility location” (RWFL) problem in a gene (or protein) interaction network, which differs from the standard facility location problem by its use of an alternative distance measure: “multi-hitting time”, the expected length of the shortest random walk from any one of the set of sequence-altered genes to an expression-altered target gene. HIT'nDRIVE reduces RWFL problem to weighted multiset cover (WMSC) problem which it solves using integer linear programming (ILP).
This is a network propagation based algorithm (Read extensive review on the topic) that identifies the influential nodes in the network. It may have many potential applications in the area of complex disease research; beyond cancer. If anyone is interested in extensive application of our algorithm, we would be very happy to extend our help. Please feedback for any suggestions.
Video [Tutorial talk]: https://youtu.be/29zZoYLDnwk (Presented at the UCLA Computational Genomics Summer Institute)
Video [seminar talk]: https://youtu.be/Ty3kgTCW9mQ
Slides [for the video above]: http://raunakms.github.io/pdf/HITnDRIVE_VanBUG_2016_11_03.pdf
Shrestha et al. (2014) HIT’nDRIVE: Multi-driver gene prioritization based on hitting time. In Sharan R, editor, Research in Computational Molecular Biology: 18th Annual International Conference, RECOMB 2014, Pittsburgh, PA, USA, April 2-5, 2014, Proceedings, pages 293-306. Springer International Publishing.