Inferring the functional effect of gene expression changes in signaling pathways.

TitleInferring the functional effect of gene expression changes in signaling pathways.
Publication TypeJournal Article
Year of Publication2013
AuthorsSebastián-Leon, P, Carbonell, J, Salavert, F, Sánchez, R, Medina, I, Dopazo, J
JournalNucleic Acids Res
Volume41
IssueWeb Server issue
PaginationW213-7
Date Published2013 Jul
ISSN1362-4962
KeywordsAnimals; Humans; Internet; Mice; Models, Statistical; Receptors, Cell Surface; Signal Transduction; Software; Transcriptome
Abstract

Signaling pathways constitute a valuable source of information that allows interpreting the way in which alterations in gene activities affect to particular cell functionalities. There are web tools available that allow viewing and editing pathways, as well as representing experimental data on them. However, few methods aimed to identify the signaling circuits, within a pathway, associated to the biological problem studied exist and none of them provide a convenient graphical web interface. We present PATHiWAYS, a web-based signaling pathway visualization system that infers changes in signaling that affect cell functionality from the measurements of gene expression values in typical expression microarray case-control experiments. A simple probabilistic model of the pathway is used to estimate the probabilities for signal transmission from any receptor to any final effector molecule (taking into account the pathway topology) using for this the individual probabilities of gene product presence/absence inferred from gene expression values. Significant changes in these probabilities allow linking different cell functionalities triggered by the pathway to the biological problem studied. PATHiWAYS is available at: http://pathiways.babelomics.org/.

DOI10.1093/nar/gkt451
PubMed ID23748960
PubMed Central IDPMC3692130