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An identical analysis using the GO class: biological processes identified several genes belonging to the steroid and lipid metabolic processes to be significantly (p<0.01) over-represented among the up-regulated set and those very specifically involved in diverse aspects of the overall immune response to be significantly (p<0.01) over represented in the down-regulated set of genes (Table S2).
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The web tool CateGOrizer [ 40] was used for grouping and counting GO classes using the GO-Slim method [ 41].
As class labels for the proteins included in Eukarya-net we used the GO annotations available in STRING (version 9.05).
We subsequently identified the GO classes, using the GOstats package in Bioconductor [ 16], that were significantly over-represented in the sets of up-or down-regulated genes in each of the samples, ordered according to temperature sum/leaf developmental stage.
The GO classes are not mutually exclusive.
The GO classes were first sorted by their relative enrichment.
Using the webtool CateGOrizer, GO classes were grouped in a total of 112 Go-Slim terms including biological process (62.1%), molecular function (25.3%) and cellular component (12.6%) ontologies.
Using the web tool CateGOrizer, GO classes were grouped into a total of 124 GO-Slim terms, which included biological process (53%), molecular function (25%) and cellular component (22%) ontologies.
We performed Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and gene ontology (GO) analyses using the list of 4648 Class A BOPs differentially methylated between DS and DSS (Table 1).
Well -- may I use the word "class"?
Use the String class's split method.
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