Supplementary data for Sun et al., "Divergence in ABA gene regulatory network underlies differential growth control"

<strong>Update (Feb. 2nd, 2022): </strong>Supplementary data S3 was revised in response to the second peer review, to include gene set enrichment analyses (GSEA) among ABA- and salt-responsive DEG sets. <strong>Update (Sep. 8th, 2021): </strong>Supplementary data S1, S4, and S8 were revised in response to peer reviewers' comment, as follows:<br> - data S1 was revised to include columns indicating orthologs included in AREB/ABF GRN. - data S4 was revised to include additional worksheets showing full results and selected examples for PiP analyses performed on genes included in AREB/ABF GRN and their ortholog pairs. - data S8 was revised to include genes in ABA-related pathways, in addition to previous lists of auxin- and ethylene-related pathways. Currently the zipped archive included both the original and revised data files for reviewing purpose. Upon publication of the manuscript, the archive will have only the final versions. <strong><br> data S1. All 1-to-1 Orthologous groups with functional genomics data from RNA-seq and DAP-seq.</strong> ABA-responsive gene expression and number of DAP-seq peaks in adjacent genomic regions for 15,198 all unambiguous 1-to-1 ortholog groups. <strong>data S2. An analysis with OrthNet (including duplicates) with functional genomics data from RNA-seq and DAP-seq.</strong> An expanded version of data S1 where all genes, including lineage(s)-specific duplicates and those not in 1-to-1 ortholog groups, organized into OrthNet units based on both sequence similarity and co-linearity. See legend inside the Dataset for details. <strong>data S3. GO enrichment among ABA-induced and repressed DEGs.</strong> A matrix of GO terms enriched in ABA-induced and repressed DEGs for all species, tissues, and time points. <strong>data S4. Phylogenetically informed profiling (PiP) analysis of ABA-responsive gene expression for the four crucifer species.</strong> Results of PiP analysis identifying GO terms showing lineage(s)-specific modifications of ABA-responses. See legend inside the Dataset for details. <strong>data S5. JASPAR motifs enriched among promoters of ABA-induced and repressed DEGs.</strong> A matrix of known transcription factor-binding motifs, obtained from the JASPAR database, enriched in the promoters of ABA-induced and repressed DEGs for all species, tissues, and time points. <strong>data S6. All DAP-Seq peak coordinates with annotations.</strong> All DAP-Seq peak coordinates with number of replicates, types of AREB/ABFs, and other information. <strong>data S7. Conserved ABA GRN.</strong> All genes curated to build the conserved ABA GRN shown in figure 4. <strong>data S8. ABA, Auxin and Ethylene GRN.</strong> All genes curated on the ABA, Auxin and ethylene pathway. 1:1 orthologs identified from RNA-seq and DAP-seq datasets were used to construct the actual GRN. <br>

<strong>（2022年2月2日更新）</strong>：为响应第二次同行评审意见，对补充数据S3进行了修订，新增了针对脱落酸（ABA）与盐胁迫响应差异表达基因（Differentially Expressed Gene，DEG）集的基因集富集分析（Gene Set Enrichment Analysis，GSEA）内容。
<strong>（2021年9月8日更新）</strong>：为响应同行评审意见，对补充数据S1、S4及S8进行了修订，具体如下：
- 补充数据S1修订后新增了标注ABA响应元件结合蛋白/ABRE结合因子（AREB/ABF）基因调控网络（Gene Regulatory Network，GRN）中直系同源基因的列项。
- 补充数据S4修订后新增了工作表，用于展示针对AREB/ABF基因调控网络及其直系同源对基因所开展的系统发育适配分析（Phylogenetically Informed Profiling，PiP）的完整结果与精选示例。
- 补充数据S8修订后在原生长素与乙烯相关通路基因列表基础上，新增了ABA相关通路基因。
当前压缩归档包含用于评审的原始版本与修订版本文件；待论文正式发表后，归档中将仅保留最终版本文件。
<strong>补充数据S1：包含RNA测序（RNA-seq）与DNA亲和纯化测序（DAP-seq）功能基因组学数据的所有1:1直系同源基因簇</strong>：涵盖15198个明确的1:1直系同源基因簇，包含各簇的ABA响应基因表达量及其邻近基因组区域的DAP-seq峰数量信息。
<strong>补充数据S2：包含RNA-seq与DAP-seq功能基因组学数据的OrthNet分析结果（含重复基因）</strong>：本数据为补充数据S1的扩展版本，将所有基因（包括谱系特异性重复基因以及未归入1:1直系同源基因簇的基因）基于序列相似性与共线性关系整合至OrthNet单元中，详细说明请参见数据集内的图例。
<strong>补充数据S3：ABA诱导与抑制型差异表达基因的GO富集分析结果</strong>：涵盖所有物种、组织与时间点下，ABA诱导型与抑制型DEG中富集的基因本体（GO）条目矩阵。
<strong>补充数据S4：四种十字花科物种ABA响应基因表达的PiP分析结果</strong>：本数据为PiP分析结果，用于鉴定ABA响应通路中存在谱系特异性修饰的GO条目，详细说明请参见数据集内的图例。
<strong>补充数据S5：ABA诱导与抑制型差异表达基因启动子区富集的JASPAR基序</strong>：涵盖所有物种、组织与时间点下，ABA诱导型与抑制型DEG启动子区富集的已知转录因子结合基序矩阵，数据来源于JASPAR数据库。
<strong>补充数据S6：带注释的所有DAP-seq峰坐标信息</strong>：包含所有DAP-seq峰的坐标信息，以及重复实验次数、AREB/ABF类型等相关注释内容。
<strong>补充数据S7：保守型ABA基因调控网络</strong>：包含经人工整理筛选、用于构建图4所示保守型ABA GRN的全部基因。
<strong>补充数据S8：ABA、生长素与乙烯基因调控网络</strong>：包含经人工整理筛选的ABA、生长素与乙烯通路上的全部基因，本研究通过RNA-seq与DAP-seq数据集鉴定得到的1:1直系同源基因被用于构建该基因调控网络。