4ArrayExpress Uploader0human6SW620RAF1 knockdown6SW480RAF1 knockdown5SW620RAF1 knockdown5SW480RAF1 knockdown4SW620RAF1 knockdown4SW480RAF1 knockdown3SW620RAF1 knockdown3SW480RAF1 knockdown2SW620RAF1 knockdown2SW480RAF1 knockdown1SW620RAF1 knockdown1SW480RAF1 knockdown6SW620NGFR knockdown6SW480NGFR knockdown5SW620NGFR knockdown5SW480NGFR knockdown4SW620NGFR knockdown4SW480NGFR knockdown3SW620NGFR knockdown3SW480NGFR knockdown2SW620NGFR knockdown2SW480NGFR knockdown1SW620NGFR knockdown1SW480NGFR knockdown6SW620MAPK3 knockdown6SW480MAPK3 knockdown5SW620MAPK3 knockdown5SW480MAPK3 knockdown4SW620MAPK3 knockdown4SW480MAPK3 knockdown3SW620MAPK3 knockdown3SW480MAPK3 knockdown2SW620MAPK3 knockdown2SW480MAPK3 knockdown1SW620MAPK3 knockdown1SW480MAPK3 knockdown6SW620MAPK1 knockdown6SW480MAPK1 knockdown5SW620MAPK1 knockdown5SW480MAPK1 knockdown4SW620MAPK1 knockdown4SW480MAPK1 knockdown3SW620MAPK1 knockdown3SW480MAPK1 knockdown2SW620MAPK1 knockdown2SW480MAPK1 knockdown1SW620MAPK1 knockdown1SW480MAPK1 knockdown6SW620MAP2K2 knockdown6SW480MAP2K2 knockdown5SW620MAP2K2 knockdown5SW480MAP2K2 knockdown4SW620MAP2K2 knockdown4SW480MAP2K2 knockdown3SW620MAP2K2 knockdown3SW480MAP2K2 knockdown2SW620MAP2K2 knockdown2SW480MAP2K2 knockdown1SW620MAP2K2 knockdown1SW480MAP2K2 knockdown6SW620MAP2K1 knockdown6SW480MAP2K1 knockdown5SW620MAP2K1 knockdown5SW480MAP2K1 knockdown4SW620MAP2K1 knockdown4SW480MAP2K1 knockdown3SW620MAP2K1 knockdown3SW480MAP2K1 knockdown2SW620MAP2K1 knockdown2SW480MAP2K1 knockdown1SW620MAP2K1 knockdown1SW480MAP2K1 knockdown6SW620HRAS knockdown6SW480HRAS knockdown5SW620HRAS knockdown5SW480HRAS knockdown4SW620HRAS knockdown4SW480HRAS knockdown3SW620HRAS knockdown3SW480HRAS knockdown2SW620HRAS knockdown2SW480HRAS knockdown1SW620HRAS knockdown1SW480HRAS knockdown4SW620control.nontrans4SW480control.nontrans2SW620control.nontrans2SW480control.nontrans1SW620control.nontrans1SW480control.nontrans6SW620control.nontarget6SW480control.nontarget5SW620control.nontarget5SW480control.nontarget4SW620control.nontarget4SW480control.nontarget3SW620control.nontarget3SW480control.nontarget2SW620control.nontarget2SW480control.nontarget1SW620control.nontarget1SW480control.nontarget6SW620control.ev6SW480control.ev5SW620control.ev5SW480control.ev4SW620control.ev4SW480control.ev3SW620control.ev3SW480control.ev2SW620control.ev2SW480control.ev1SW620control.ev1SW480control.ev6SW620CDK5 knockdown6SW480CDK5 knockdown5SW620CDK5 knockdown5SW480CDK5 knockdown4SW620CDK5 knockdown4SW480CDK5 knockdown3SW620CDK5 knockdown3SW480CDK5 knockdown2SW620CDK5 knockdown2SW480CDK5 knockdown1SW480CDK5 knockdown2183arrayexpress_sidhttp://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-53091Although many methods have been developed for inference of biological networks, the validation of the resulting models has largely.../profile/8773/arrayexpressuploader3125cancercellcolorectal cancerlineDec.12, 2014Falseinference-and-validation-of-predictive-gene-networE-GEOD-53091_A-AFFY-44Inference and validation of predictive gene networks from biomedical literature and gene expression dataJul.11, 2014Although many methods have been developed for inference of biological networks, the validation of the resulting models has largely remained an unsolved problem. Here we present a framework for quantitative assessment of inferred gene interaction networks using knock-down data from cell line experiments. Using this framework we are able to show that network inference based on integration of prior knowledge derived from the biomedical literature with genomic data significantly improves the quality of inferred networks relative to other approaches. Our results also suggest that cell line experiments can be used to quantitatively assess the quality of networks inferred from tumor samples. Knock-down of eight genes were performed on colorectal cancer cell lines to identify the genes whose expression was significantly affected. These genes were subsequently used to validate the quality of our causal gene interaction network.E-GEOD-53091http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-53091/samples/