VToD Voting based cancer module identification by combining topological and data-driven properties

 

  
News
2013/04/13: Source codes are uploaded.
Introductionon
It integrates Copy Number Aberration (CNA) and Gene Expression (GE) data using direct and indirect relationships among gene pairs in a form of Gene-Gene Relationship Network (GGR). Genes from differential expression and significantly altered regions are used in the network GGR. Coupling GGR as a source of pair-wise data-driven properties among gene pairs with PPI as topological one, VToD detects cancer related modules/pathways with higher precision.
Paper Azad, A.K.M. and Lee, H. (2013) Voting based cancer module identification by combining topological and data-driven properties.
Source codes
Codes were implemented in .Net Platform and are available here. Instructions for running source codes are here. Input files for these codes are provided here excluding the preprocessed CNAs and GE data sets.
Data sets

Paired CNAs and GE data sets were collected from TCGA data portal for Glioblastoma Multiforme (GBM) patients at 24th July, 2011. Again, for Ovarian Serous Cystadenocarcinoma (OVC) patients, paired CNAs and GE data sets were also collected from TCGA data portal at 25th June, 2012. Both GBM and OVC cancer data sets were preprocessed. PPI data set were collected from Cerami et al., 2010. Contact us if preprocessed data sets (Both CNAs and GE) need to be collected.
Contacts
hyunjulee at gist.ac.kr, azad at gist.ac.kr