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.