To analyze any differential expression in the IGROV1 cell lines, a generalized linear model likelihood ratio test was used. Specifically, a negative binomial generalized linear model was fitted, with shRNA-wise or gene-wise dispersions estimated using the Cox-Reid profile-adjusted likelihood method. Then, a likelihood ratio test was employed to check the differential expression50 (link). The dispersion estimation, model fitting, and testing were implemented using the functions estimateDisp(), glmFit () and glmLRT(), respectively, in the edgeR package51 (link)To interpret the testing results in a biological context, gene ontology (GO) enrichment analysis and KEGG pathway enrichment analysis were employed as downstream procedures, using the online available tool Enrichr52 (link).
For pathological analysis, IHC images were analyzed by Histoquant software (3D Histech).
The remaining experiments were repeated at least three times and representative data/images are shown. Statistical analysis was performed using GraphPad Prism software, presented as mean ± SEM. For comparisons between two groups, P values were calculated. P values of 0.05 (*), 0.01 (**),0.001 (***) and 0.0001(****) were considered statistically significant.
For pathological analysis, IHC images were analyzed by Histoquant software (3D Histech).
The remaining experiments were repeated at least three times and representative data/images are shown. Statistical analysis was performed using GraphPad Prism software, presented as mean ± SEM. For comparisons between two groups, P values were calculated. P values of 0.05 (*), 0.01 (**),0.001 (***) and 0.0001(****) were considered statistically significant.
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