Research output: Contribution to journal › Article › peer-review
Genome-wide map of human and mouse transcription factor binding sites aggregated from ChIP-Seq data 06 Biological Sciences 0604 Genetics. / Vorontsov, Ilya E.; Fedorova, Alla D.; Yevshin, Ivan S. et al.
In: BMC Research Notes, Vol. 11, No. 1, 756, 23.10.2018, p. 756.Research output: Contribution to journal › Article › peer-review
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TY - JOUR
T1 - Genome-wide map of human and mouse transcription factor binding sites aggregated from ChIP-Seq data 06 Biological Sciences 0604 Genetics
AU - Vorontsov, Ilya E.
AU - Fedorova, Alla D.
AU - Yevshin, Ivan S.
AU - Sharipov, Ruslan N.
AU - Kolpakov, Fedor A.
AU - Makeev, Vsevolod J.
AU - Kulakovskiy, Ivan V.
N1 - Publisher Copyright: © 2018 The Author(s).
PY - 2018/10/23
Y1 - 2018/10/23
N2 - Objectives: Mammalian genomics studies, especially those focusing on transcriptional regulation, require information on genomic locations of regulatory regions, particularly, transcription factor (TF) binding sites. There are plenty of published ChIP-Seq data on in vivo binding of transcription factors in different cell types and conditions. However, handling of thousands of separate data sets is often impractical and it is desirable to have a single global map of genomic regions potentially bound by a particular TF in any of studied cell types and conditions. Data description: Here we report human and mouse cistromes, the maps of genomic regions that are routinely identified as TF binding sites, organized by TF. We provide cistromes for 349 mouse and 599 human TFs. Given a TF, its cistrome regions are supported by evidence from several ChIP-Seq experiments or several computational tools, and, as an optional filter, contain occurrences of sequence motifs recognized by the TF. Using the cistrome, we provide an annotation of TF binding sites in the vicinity of human and mouse transcription start sites. This information is useful for selecting potential gene targets of transcription factors and detecting co-regulated genes in differential gene expression data.
AB - Objectives: Mammalian genomics studies, especially those focusing on transcriptional regulation, require information on genomic locations of regulatory regions, particularly, transcription factor (TF) binding sites. There are plenty of published ChIP-Seq data on in vivo binding of transcription factors in different cell types and conditions. However, handling of thousands of separate data sets is often impractical and it is desirable to have a single global map of genomic regions potentially bound by a particular TF in any of studied cell types and conditions. Data description: Here we report human and mouse cistromes, the maps of genomic regions that are routinely identified as TF binding sites, organized by TF. We provide cistromes for 349 mouse and 599 human TFs. Given a TF, its cistrome regions are supported by evidence from several ChIP-Seq experiments or several computational tools, and, as an optional filter, contain occurrences of sequence motifs recognized by the TF. Using the cistrome, we provide an annotation of TF binding sites in the vicinity of human and mouse transcription start sites. This information is useful for selecting potential gene targets of transcription factors and detecting co-regulated genes in differential gene expression data.
KW - ChIP-Seq
KW - Cistrome
KW - Human and mouse
KW - Regulatory regions
KW - Target genes
KW - Transcription factor binding sites
KW - Humans
KW - Sequence Analysis, DNA
KW - Animals
KW - Mice
KW - Transcription Factors
KW - Genome
KW - Binding Sites
UR - http://www.scopus.com/inward/record.url?scp=85055601897&partnerID=8YFLogxK
U2 - 10.1186/s13104-018-3856-x
DO - 10.1186/s13104-018-3856-x
M3 - Article
C2 - 30352610
AN - SCOPUS:85055601897
VL - 11
SP - 756
JO - BMC Research Notes
JF - BMC Research Notes
SN - 1756-0500
IS - 1
M1 - 756
ER -
ID: 17248664