Integrated maize cis-regulatory elements (iCREs)

Files containing the genomic coordinates of the conserved non-coding sequences (BLSSpeller, msa_pipeline, funTFBS, and Song-2021), the accessible chromatin regions (ACRs) and the unmethylated regions (UMRs) in the maize genome version 5 employed to generate the integrated cis-regulatory-elements (iCREs), both the all and maxF1 sets. Version 1.1 includes the "all" iCREs and the "maxF1" iCREs annotated to their closest gene. Version 1.2 includes an extra version of the same files as the previous one but with the genome coordinates in the maize genome version 4 (AGPv4) Version 1.3 includes the "all" iCREs and the "maxF1" iCREs annotated to their closest gene in the coordinates of the maize genome version 4 (AGPv4). Version 1.4 includes Supplementary Table 3 and 4 (which in the reserach chapter version of the article, included in the doctoral dissertation of Nicolás Manosalva, they correspond to Supporting Datasets 5 and 6): Table S3/Dataset S5: Gene ontology (GO) enrichment of the genes associated with different repetitive element types and transposable element (TE) superfamilies that are found within iCREs. Table S4/Dataset S6: Number of, median value of the transcripts per million, and p-value of the genes associated with TEs within, outside, and within and outside iCREs. The computations were binned per distance to the closest gene.