title: Inferring the functional effect of gene expression changes in signaling pathways.
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/.
authors.affiliation: Department of Computational Genomics, Centro de Investigación Príncipe Felipe, Valencia 46012, Spain.
authors.forename: Patricia
authors.initials: P
authors.lastname: Sebastián-León
authors.forename: José
authors.initials: J
authors.lastname: Carbonell
authors.forename: Francisco
authors.initials: F
authors.lastname: Salavert
authors.forename: Rubén
authors.initials: R
authors.lastname: Sanchez
authors.forename: Ignacio
authors.initials: I
authors.lastname: Medina
authors.forename: Joaquín
authors.initials: J
authors.lastname: Dopazo
mesh_terms: D000818:Animals; D006801:Humans; D020407:Internet; D051379:Mice; D015233:Models, Statistical; D011956:Receptors, Cell Surface / Q000378:metabolism; D015398:Signal Transduction / Q000235:genetics*; D012984:Software; D059467:Transcriptome
chemical_list: D011956:Receptors, Cell Surface