The majority of these studies, mainly of Anglo-Saxon origin, investigate the different factors which affect the efficacy of ACs and usually focus their analysis on listed companies.
These primarily involved post-hoc functional analyses such as T-test, ANOVA [22] or clustering analyses [23] (i.e first finding lists of changed genes, by various computational methods, and then conducting functional enrichment analysis on these lists, e.g. EASE [24] and MAPPFinder [25]).
GO (gene ontology) analysis on these lists was then carried out by performing functional annotations of genes using DAVID Bioinformatics [ 24, 25] and further grouped into their parent GO term using CateGOrizer [ 26].
To understand the genes regulated by ZNF217 and the pathways associated with ERα function, we performed gene ontology analysis on the lists of differentially regulated genes following ZNF217 silencing with the GREAT classification gene ontology tool [ 16].
To identify biological pathways perturbed by combined docetaxel chemotherapy with ADT, we performed an enrichment analysis on our lists of up- and down-regulated genes (FDR < 0.05) using 3 different pathways analysis tools: the KEGG (Kyoto Encyclopedia of Genes and Genomes) database [ 26]; IPA Core Analysiss" function; and Metacore.
Manual analysis on the list of 55 false positives confirms that one or more proteins remain unidentified in 30 sentences in the preprocessing steps.
We therefore based our analysis on a list of over 1000 chemicals used in fracking, as reported by USEPA (2012a) (this list is given in the supplementary information).
When carrying out GO ontology analysis on the list of Cluster 3 signature genes downregulated in the infarcted epicardium, we observed similar enrichment of GO lists as for the initial epicardial gene analysis, such as acute inflammatory response (GO 2526), complement activation (GO 6956), innate immune response (45087), and inflammatory response (GO 2541) (Table S4).
DAVID analysis on this list of genes revealed a significant down regulation of only one set of genes involved in proteolysis (Table 4).
