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>