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Human and mouse cistromes: genomic maps of putative cis-regulatory regions bound by transcription factors

posted on 2018-10-17, 15:22 authored by Ilya E. Vorontsov, Alla D. Fedorova, Ivan S. Yevshin, Ruslan N. Sharipov, Fedor A. Kolpakov, Vsevolod J. Makeev, Ivan V. Kulakovskiy
This dataset consists of 1 .xlsx file and 8 .zip files:
- cistrome_overview.xlsx is an Excel spreadsheet containing the computational protocol of the cistrome aggregation in the 1st tab, and overviews of the resulting cistrome maps for mouse and human in the 2nd and 3rd tabs.
- cistrome_hg19.zip, cistrome_hg38.zip, cistrome_mm9.zip and cistrome_mm10.zip contain genome-wide cistome genomic maps for human (hg19 and hg38) and mouse (mm9 and mm10) genome assemblies. Each .zip file contains two folders: one for the base cistrome and another for the motif-annotated subset. The contents of these folders are .bed files.
- cistrome2genes_hg19.zip, cistrome2genes_hg38.zip, cistrome2genes_mm9.zip and cistrome2genes_mm10.zip contain gene-centric maps for the respective human and mouse genome assemblies, annotated with the transcription start sites (TSS) using the GENCODE reference data. The gene lists include only the genes with cistrome regions located not farther than 10kb from TSS. These are .tsv files.
- Inside each .zip file, there is a separate text (.txt) file with a technical description of contents and file naming conventions.

The related manuscript describes the objectives, sourcing and processing of the data provided here in greater detail. In short, the objective is to present general genome-wide maps of putative cis-regulatory regions bound by transcription factors for human and mouse cistromes. This is achieved through systematic analysis of ChIP-Seq data obtained from the Gene Transcription Regulation Database (http://gtrd.biouml.org) and sequence motifs from the HOmo sapiens COmprehensive MOdel COllection (HOCOMOCO: http://hocomoco.autosome.ru).


The human cistrome construction was supported by the Russian Science Foundation grant to I.V.K. [17-74-10188]. The mouse cistrome construction was supported by the Program of fundamental research for state academies for 2013-2020 years (No 01201363825) and by Presidium of the Russian Academy of Sciences program in molecular and cellular biology. Development of motif annotation tools was supported by the Russian Science Foundation grant 14-50-00060. I.E.V. was personally supported by the Skoltech Systems Biology Fellowship.


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