Functional clusters in rice, grape and Arabidopsis

<b>1) R</b><b>aw data folder:</b> 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).<br>2)<b> Summary (SUMS) data folder:</b> Contains spreadsheets summaries of the raw data, including:<br>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.<i><br></i><i><br></i>b)<i> </i>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).<br><b><br></b><b>3) Common and specific GOs file</b>: the file details commonalties vs. specificities among GO tags for one genome or combination of genomes at <i>P-</i>value 1e^-6 and 40, 70, 90 and 98 % stringencies. Durum wheat GOs are also included for comparative purposes.<br><br><b>4) BLAST2GO-pro annotations</b> used for the pipeline (rice, vitis, and arabidopsis)<br><b>5) selected genome snapshots</b> of FNTDC patterning at intermediate conditions (<i>setting_2 </i>; 70% identity, ratio 0.7, <i>P-value</i> of 1e^-6). Snapshots covering further settings (for each setting, several image resolutions are available ) can be found within each specific raw data folder.