An integrative analysis of gene expression and molecular interaction data to identify dys-regulated sub-networks in inflammatory bowel disease

BMC Bioinformatics
Daniele Muraro, Alison Simmons

Abstract

Inflammatory bowel disease (IBD) consists of two main disease-subtypes, Crohn's disease (CD) and ulcerative colitis (UC); these subtypes share overlapping genetic and clinical features. Genome-wide microarray data enable unbiased documentation of alterations in gene expression that may be disease-specific. As genetic diseases are believed to be caused by genetic alterations affecting the function of signalling pathways, module-centric optimisation algorithms, whose aim is to identify sub-networks that are dys-regulated in disease, are emerging as promising approaches. In order to account for the topological structure of molecular interaction networks, we developed an optimisation algorithm that integrates databases of known molecular interactions with gene expression data; such integration enables identification of differentially regulated network modules. We verified the performance of our algorithm by testing it on simulated networks; we then applied the same method to study experimental data derived from microarray analysis of CD and UC biopsies and human interactome databases. This analysis allowed the extraction of dys-regulated subnetworks under different experimental conditions (inflamed and uninflamed tissues in CD and ...Continue Reading

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Citations

Nov 2, 2017·Expert Opinion on Drug Discovery·Carolina L BelleraAlan Talevi
Sep 14, 2017·Molecular Diagnosis & Therapy·Eleni Stylianou
Mar 18, 2021·American Journal of Human Genetics·Diptavo DuttaSeunggeun Lee
Aug 31, 2021·PLoS Computational Biology·Elva María Novoa-Del-ToroAnaïs Baudot

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Methods Mentioned

BETA
biopsies
biopsy

Software Mentioned

iRefWeb
Gene Set Enrichment Analysis ( GSEA )
GSEA
qquad
GEO2R R script
MPact

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