Interactome-Transcriptome Integration Method in Molecular Biology Book chapter

This page contains supplementary material for the chapter entitled Detection of driver protein complexes in breast cancer metastasis by large scale transcriptome-interactome integration. This chapter deals with the pratical use of the Interactome-Transcriptome Integration Project.

This book chapter was authored by M. Garcia, P. Finetti, F. Bertucci, D. Birnbaum and G. Bidaut.

In this chapter, we are describing an interactome-based algorithm, Interactome-Transcriptome Integration (ITI) that is used to find a generalizable signature for prediction of breast cancer relapse by superimposition of a large scale protein-protein interaction data (human interactome) over several gene expression datasets. ITI extracts regions in the interactome whose expressions are discriminating for predicting relapse-free survival in cancer and allow detection of subnetworks that constitutes a generalizable and stable genomic signature (Garcia et al., 2012). In this chapter, we describe the practical aspects of running the full ITI pipeline (subnetwork detection and classification) on 6 microarray datasets.

ITI Code

The ITI version used in this chapter is the 2.0, available here.

Supplementary Data

Directory structure [iti-study.tar.gz].
Interactome data [interactomes-2012.tar.gz].
Breast cancer transcriptome data [breast_cancer_2012.tar.gz].
Annotations [annotations-iti-ncbi.tar.gz].
Resourcerer annotations [resourcerer.tar.gz].

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