The primary core analysis included all 8,010 patients but did not include any events after the first 2 years (the time of the switch) for patients in the two sequential arms [ 43].
The routine core data analysis included permeability, porosity and lithology descriptions.
BAIT provides a core framework for Strand-seq analysis, including functionality to plot W and C template strands, count aneuploid chromosomes, and map and enumerate SCE events (see Additional file 1: Figure S1).
The mapped datasets containing either up-regulated or down-regulated genes in HT29 or GC3/c1 cells with corresponding expression values were subjected to core analysis that includes overall canonical pathway enrichment analysis.
To gain insight into the liver tissue processes that differed between groups, the list of the differentially-expressed genes was explored using the core analysis function included in Ingenuity Pathways Analysis (IPA).
The "Core Analysis" function included in Ingenuity Pathway Analysis (IPA) (Ingenuity Systems Inc , USA [ 52] was used to aid interpretation of the hypo- and hyper-methylated (fold change > 1.5) genes found by comparison of zebrafish HCC with healthy liver.
To gain insight on the functions of the blood transcriptome that differed significantly between the H and L groups, we measured the subsets of DE genes by using the core analysis function included in Ingenuity Pathways Analysis (IPA).
To gain insight into the metabolic processes that differed between both groups, the list of 396 differentially expressed genes was analyzed using the core analysis function included in Ingenuity Pathways Analysis (IPA).
The accessions of these genes were imported into IPA, then the "Core Analysis" function included in IPA was used to analyze the genes in the context of networks, biological functions, and canonical pathways.
The global list of 256 DE genes affected by genetic type and the two partial lists of 102 and 154 genes upregulated in IB and DU×IB, respectively, were explored using both the DAVID tool and the core analysis function included in IPA Analysis.
