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.

1) 原始数据文件夹（Raw data folder）：针对每个候选聚类，包含基因本体（Gene Ontology, GO）富集分析数据（含GO超几何检验结果及相关统计量）、携带GO注释的基因与全部基因的注释详情（含topBLAST比对结果、功能注释、关联GO条目）、剔除同源性基因的相关信息，以及匹配基因本体生物过程（Gene Ontology Biological Process, GO-BP）的基因的配套BLAST输出文件与蛋白质比对文件（要求BLAST期望值≤1×10⁻¹⁰）。
2) 汇总（SUMS）数据文件夹：包含原始数据的电子表格汇总文件，具体包括：
a) 单样本汇总文件：针对每个实验条件与基因组，汇总从每个FNTDC原始数据文件夹下的7个文件中获取的全部核心数据。
b) 合并汇总文件：覆盖特定基因组子集、基因组组合或实验条件的汇总结果（例如全部基因组与全部实验条件、仅单个基因组搭配全部实验条件、全部基因组搭配严格筛选条件等）。
3) 通用与特异性GO条目文件：该文件详细阐述了在P值（P-value）阈值为1×10⁻⁶、序列一致性分别为40%、70%、90%与98%的筛选严格度下，单个基因组或基因组组合间GO条目的共性与特异性；为便于对比分析，同时纳入了硬粒小麦的GO条目。
4) 本次分析流程所用的BLAST2GO-pro注释文件（覆盖水稻、葡萄与拟南芥）。
5) 中间参数条件下FNTDC模式的选定基因组快照：对应参数为setting_2（70%序列一致性、比对覆盖比例0.7、P值1×10⁻⁶）。其他参数设置对应的快照（每个参数设置均提供多种图像分辨率）可在各对应原始数据文件夹中获取。