Interactome-Transcriptome Integration

This is the new location for the Interactome-Transcriptome Integration Project, Developed by the Cibi Bioinformatics Platform at the Centre de Recherche en Cancerologie de Marseille(CRCM). As ITI moved forward, we switched from a lab-based hosting to Sourceforge.

ITI allows integrated gene expression data analysis using protein-protein interaction data as prior. It returns regions of the human interactome that are differentially expressed between two conditions over several datasets. It has been published in two projects: An unsupervised analysis (Project 1), and a supervised analysis (Project 2).

An integrated analysis with Comprehensive Genomics Hybridization profiles is currently under development.

ITI-based Projects

Project 1: Breast Cancer Analysis (February 2010)
Project 2: Breast Cancer Classification (February 2012)
Project 3: Integrated GCH-ITI (CITI) analysis (Not yet completed)

Documentation & Downloads

Downloads links are here.
Supplementary material for Methods on Molecular Biology book chapter is available here.
Our poster at JOBIM 2012: [PDF]
Slides for a talk that was given at the 1st CRCL Scientific Department Day, May 15th, 2012 in Lyon, France: [Lien Slideshare]
Installation and usage instructions are available from the Wiki.

Papers

M. Garcia, O. Stahl, P. Finetti, D. Birnbaum, F. Bertucci, and Bidaut, G. Linking interactome to disease: a network-based analysis of metastatic relapse in breast cancer, in Handbook of Research on Computational and Systems Biology: Interdisciplinary Applications. 2010, pp 406-427. L.A. Liu, D Wei, Y. Li, H. Lei Editors. IGI Global.
Garcia M, Millat-Carus R, Bertucci F, Finetti P, Birnbaum D, Bidaut G. Interactome- Transcriptome integration for predicting distant metastasis in breast cancer. Bioinformatics. 2012 Mar 1;28(5):672-8.
M. Garcia, P. Finetti, F. Bertucci, D. Birnbaum and G. Bidaut. Detection of driver protein complexes in breast cancer metastasis by large scale transcriptome-interactome integration. Methods in Molecular Biology (in press)

Project funded by

Project hosted by

Questions? Comments? Do not hesitate to contact us from the Cibi home page.