RSeqFlow-OlivePollen8 - OE-PBs.zip: Enriched biological processes in time contrasts.

A compressed file containing the biological processes up- and down-regulated in each time contrast as a tab separated list. Columns in each file correspond to: • ID: the GO code. • Description: explanation of the ID. • GeneRatio: ratio of DEGs annotated in the ID term respect to the total number of DEGs in this contrast. • BgRatio: ratio of all genes that are annotated in this ID term respect to the total number of genes in the organism (i.e., A. thaliana). • pvalue: reliability of enrichment. • p.adjusted: Benjamini and Hochberg’s multitasking adjustment of P-values. • qvalue: John Storey’s estimation of the false discovery rate by the R package qvalue. • GenID: TAIR10 code of A. thaliana orthologues for DEGs belonging to the ID term. • Count: number of TAIR codes in the ID term. • TF: family of transcription factors present in the ID term. The fold enrichment can be easily calculated by dividing geneRatio by BgRatio.