Microarray analysis

Microarray expression data ({"type":"entrez-geo","attrs":{"text":"GSE59857","term_id":"59857"}}GSE59857) were uploaded via the GEOquery package in R programming language (28) to comprehensively analyze gene expression in 151 CRC cell lines and then to identify key cell cycle genes frequently dysregulated by the PIK3-Akt pathway. Uploaded data were loess normalized using the R Lumi package (29). Additional filtering was conducted via present in at least one (PALO) filter with a 0.01 threshold as well as low varying probes (SD <0.25). One way ANOVA model was conducted to model the “8 or 9 conditions” for differential gene expression. Linear contrasts were used to conduct the various hypothesis tests between “conditions”.