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Significantly affected biological processes identified by ToppFun Suite software on affected genes were "RNA splicing and processing" and "cell cycle" (Table 2).
Biological Processes identified by GO and associated with T4SS were also tagged, along with related concepts with alternate lexical realizations.
Prominent among the biological processes identified by pathway analysis in another study, performed two weeks after SNL, were functions such as neurite outgrowth and neuronal development, suggesting these effects to be among the primary consequences of SNL injury [37].
Significantly overrepresented biological processes identified by hypomethylated KR-DMRs.
Significantly overrepresented biological processes identified by hypermethylated KR-DMRs.
Significantly overrepresented biological processes identified by hypomethylated WT-DMRs.
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The top GO biological process identified by DAVID analysis is regulation of cell proliferation and the p80HT target genes associated with the process are listed in Table 2.
As could be expected, the different bioinformatics methods used (DAVID, Consensus Pathway and STRING databases, and ssGSEA) in this study show some degree of overlapping in the biological processes identified, but they are complementary as each one also finds some relevant unique biological processes not identified by the others.
A proportion of genes identified as significantly differentially expressed were selected for verification by QPCR, on the basis of robust microarray data confirming differential gene expression, involvement in a biological process identified as enriched by GO analysis, or a known function in neurodegeneration.
b Biological processes identified by GO annotations (DAVID) We then took advantage of Gene Ontology and GSEA to identify enriched biological pathways (Additional 11).
Enriched biological processes were identified by overrepresentation analysis based on Gene Ontology (GO) categories, which is a generally accepted procedure to achieve this.
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