PMC:4307189 / 21523-22946
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/4307189","sourcedb":"PMC","sourceid":"4307189","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4307189","text":"Drug resistant cross-talk prediction\nSince, Lapatinib is an EGFR and ErbB inhibitor, we considered the cross-talks between the EGFR/ErbB signaling pathway and other signaling pathways. Here cross-talks can be defined as any gene-pair (genei,genej) in which genei ∈ {genes in EGFR/ErbB signaling pathway} and genej ∈ {genes in other signaling pathways}, or vice versa [31]. Thus if both genes in any gene-pair were found in the same signaling pathway, that particular gene-pair was trivially ignored. For that purpose, we collected 24 signaling pathways from Reactome [32] (downloaded at 19/05/2014), 35 signaling pathways from KEGG [33,34] (downloaded at 21/10/2014), and 63 signaling pathways from WikiPathway [35] (downloaded at 16/10/2014) databases. Each signaling pathway downloaded from these databases was encoded as tab-delimitated lists of gene symbols.\nTo determine whether a given gene-pair is involved in drug resistance, we calculated a simple odds ratio of the corresponding two posterior probabilities: (10) odds=PrYij1R=1PrYij1P=1\nwhere, Yij1R and Yij1P are gene-gene relationships defined over resistant and parental networks, respectively, and the probabilities are estimated using MCMC sampling. We then selected only those gene-pairs for which the odds score and PruijR=1 are greater than conservative thresholds, and identified these as the gene-pairs which are potentially involved in drug-resistance.","divisions":[{"label":"title","span":{"begin":0,"end":36}},{"label":"p","span":{"begin":37,"end":862}},{"label":"p","span":{"begin":863,"end":1046}},{"label":"label","span":{"begin":1018,"end":1022}}],"tracks":[{"project":"2_test","denotations":[{"id":"25599599-18434343-14868125","span":{"begin":368,"end":370},"obj":"18434343"},{"id":"25599599-24243840-14868126","span":{"begin":568,"end":570},"obj":"24243840"},{"id":"25599599-12539951-14868127","span":{"begin":633,"end":635},"obj":"12539951"},{"id":"25599599-22096230-14868128","span":{"begin":712,"end":714},"obj":"22096230"}],"attributes":[{"subj":"25599599-18434343-14868125","pred":"source","obj":"2_test"},{"subj":"25599599-24243840-14868126","pred":"source","obj":"2_test"},{"subj":"25599599-12539951-14868127","pred":"source","obj":"2_test"},{"subj":"25599599-22096230-14868128","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#9fec93","default":true}]}]}}