Functional clusters in rice, grape and Arabidopsis

1) Raw data folder: Contains, for each candidate cluster, GO enrichment data (GO hypergeometric test results and related statistics), annotation details for GO-equipped and all genes (topBlast results, annotations, associated GOs), details over homology-discarded genes and accompanying Blast outputs and protein alignment files for GO-BP assigned genes (below Blast expect value 1e-10). 2) Summary (SUMS) data folder: Contains spreadsheets summaries of the raw data, including: a) Single summary files where, for each condition and genome, are summarized all main data gathered from the 7 files of each FNTDC raw data folder. b) Merged summary files covering specific subset and combinations of genomes and/or conditions (e.g. all genomes and all conditions; only one genome with all conditions; all genomes and only stringent conditions; etc). 3) Common and specific GOs file: the file details commonalties vs. specificities among GO tags for one genome or combination of genomes at P-value 1e-6 and 40, 70, 90 and 98 % stringencies. Durum wheat GOs are also included for comparative purposes. 4) BLAST2GO-pro annotations used for the pipeline (rice, vitis, and arabidopsis) 5) selected genome snapshots of FNTDC patterning at intermediate conditions (setting_2 ; 70% identity, ratio 0.7, P-value of 1e-6). Snapshots covering further settings (for each setting, several image resolutions are available ) can be found within each specific raw data folder.