Inference and validation of predictive gene networks from biomedical literature and gene expression data

摘要

Althoughmanymethodshavebeendevelopedforinferenceofbiologicalnetworks,thevalidationoftheresultingmodelshaslargelyremainedanunsolvedproblem.Herewepresentaframeworkforquantitativeassessmentofinferredgeneinteractionnetworksusingknock-downdatafromcelllineexperiments.Usingthisframeworkweareabletoshowthatnetworkinferencebasedonintegrationofpriorknowledgederivedfromthebiomedicalliteraturewithgenomicdatasignificantlyimprovesthequalityofinferrednetworksrelativetootherapproaches.Ourresultsalsosuggestthatcelllineexperimentscanbeusedtoquantitativelyassessthequalityofnetworksinferredfromtumorsamples./p/div