PMC:4307189 / 52560-54509
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":"In Netwalker analysis of our primary dataset (SKBR3 cell-line, GSE38376), we compared the expression changes of all the samples in parental conditions (basal, 0.1 μM and 1.0 μM) with those of all the samples in resistant conditions (basal, 0.1 μM and 1.0 μM). However, we conducted another experiment on both of our primary (SKBR3 cell-line, GSE38376) and secondary datasets (BT474 cell-line, GSE16179) in which we first identified genes dysregulated in treatment vs basal conditions in parental samples and then checked if those genes were reversely changed in treatment conditions in resistant samples. To that end, for each sample, first we calculated the fold-change(s) of parental treatment condition(s) compared to parental basal condition, and then we calculated the fold-changes of resistant basal and resistant treatment conditions compared to parental basal condition (Additional file 1: Figure S2A and S3A). Then, we chose only those genes for which, in any of the 3 samples, expressions were dysregulated (up-/down-regulated) in (all the) parental treatment condition(s) (log2 of fold-changes were positive/negative), and for that particular sample, expressions were reversely changed (the fold-change sign was opposite to that of parental condition) in all the resistant treatment conditions (Additional file 1: Figure S2B and S3B). This may be a strong indicator of sensitivity to an inhibitor in parental conditions and the development of acquired resistance. Next, we compared these selected genes to cross-talks found in results from GSE38379 (104, 188 and 299 EGFR/ErbB cross-talks from Reactome, KEGG and WikiPathway, respectively) and GSE16179 (83, 133 and 277 EGFR/ErbB cross-talks from Reactome, KEGG and WikiPathway, respectively). Although we didn’t find any such cross-talks overlapping with the results from the primary dataset (GSE38379), we found 401 from our secondary dataset (GSE16179) (Additional file 15: Table S14).","tracks":[]}