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.