TRED: A transcriptional regulatory element database, new entries and other development

C. Jiang; Z. Xuan; F. Zhao; M. Q. Zhang

doi:10.1093/nar/gkl1041

TRED: A transcriptional regulatory element database, new entries and other development

C. Jiang, Z. Xuan, F. Zhao, M. Q. Zhang

Research output: Contribution to journal › Article › peer-review

269 Scopus citations

Abstract

Transcriptional factors (TFs) and many of their target genes are involved in gene regulation at the level of transcription. To decipher gene regulatory networks (GRNs) we require a comprehensive and accurate knowledge of transcriptional regulatory elements. TRED (http://rulai.cshl.edu/TRED) was designed as a resource for gene regulation and function studies. It collects mammalian cis- and trans-regulatory elements together with experimental evidence. All the regulatory elements were mapped on to the assembled genomes. In this new release, we included a total of 36 TF families involved in cancer. Accordingly, the number of target promoters and genes for TF families has increased dramatically. There are 11 660 target genes (7479 in human, 2691 in mouse and 1490 in rat) and 14 908 target promoters (10 225 in human, 2985 in mouse and 1698 in rat). Additionally, we constructed GRNs for each TF family by connecting the TF-target gene pairs. Such interaction data between TFs and their target genes will assist detailed functional studies and help to obtain a panoramic view of the GRNs for cancer research.

Original language	English (US)
Pages (from-to)	D137-D140
Journal	Nucleic acids research
Volume	35
Issue number	SUPPL. 1
DOIs	https://doi.org/10.1093/nar/gkl1041
State	Published - Jan 2007
Externally published	Yes

ASJC Scopus subject areas

Genetics

Access to Document

10.1093/nar/gkl1041

Cite this

@article{863656487a704ad0949ca85b923d31b0,

title = "TRED: A transcriptional regulatory element database, new entries and other development",

abstract = "Transcriptional factors (TFs) and many of their target genes are involved in gene regulation at the level of transcription. To decipher gene regulatory networks (GRNs) we require a comprehensive and accurate knowledge of transcriptional regulatory elements. TRED (http://rulai.cshl.edu/TRED) was designed as a resource for gene regulation and function studies. It collects mammalian cis- and trans-regulatory elements together with experimental evidence. All the regulatory elements were mapped on to the assembled genomes. In this new release, we included a total of 36 TF families involved in cancer. Accordingly, the number of target promoters and genes for TF families has increased dramatically. There are 11 660 target genes (7479 in human, 2691 in mouse and 1490 in rat) and 14 908 target promoters (10 225 in human, 2985 in mouse and 1698 in rat). Additionally, we constructed GRNs for each TF family by connecting the TF-target gene pairs. Such interaction data between TFs and their target genes will assist detailed functional studies and help to obtain a panoramic view of the GRNs for cancer research.",

author = "C. Jiang and Z. Xuan and F. Zhao and Zhang, {M. Q.}",

note = "Funding Information: We thank Dr Thomas Kubarych for the critical reading of the manuscript for English. This work is supported by a contract grant from NCI and partly by a NIH grant HG001696. Funding to pay the Open Access publication charges for this article was provided by NIH/NHGRI.",

year = "2007",

month = jan,

doi = "10.1093/nar/gkl1041",

language = "English (US)",

volume = "35",

pages = "D137--D140",

journal = "Nucleic acids research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "SUPPL. 1",

}

TY - JOUR

T1 - TRED

T2 - A transcriptional regulatory element database, new entries and other development

AU - Jiang, C.

AU - Xuan, Z.

AU - Zhao, F.

AU - Zhang, M. Q.

N1 - Funding Information: We thank Dr Thomas Kubarych for the critical reading of the manuscript for English. This work is supported by a contract grant from NCI and partly by a NIH grant HG001696. Funding to pay the Open Access publication charges for this article was provided by NIH/NHGRI.

PY - 2007/1

Y1 - 2007/1

N2 - Transcriptional factors (TFs) and many of their target genes are involved in gene regulation at the level of transcription. To decipher gene regulatory networks (GRNs) we require a comprehensive and accurate knowledge of transcriptional regulatory elements. TRED (http://rulai.cshl.edu/TRED) was designed as a resource for gene regulation and function studies. It collects mammalian cis- and trans-regulatory elements together with experimental evidence. All the regulatory elements were mapped on to the assembled genomes. In this new release, we included a total of 36 TF families involved in cancer. Accordingly, the number of target promoters and genes for TF families has increased dramatically. There are 11 660 target genes (7479 in human, 2691 in mouse and 1490 in rat) and 14 908 target promoters (10 225 in human, 2985 in mouse and 1698 in rat). Additionally, we constructed GRNs for each TF family by connecting the TF-target gene pairs. Such interaction data between TFs and their target genes will assist detailed functional studies and help to obtain a panoramic view of the GRNs for cancer research.

AB - Transcriptional factors (TFs) and many of their target genes are involved in gene regulation at the level of transcription. To decipher gene regulatory networks (GRNs) we require a comprehensive and accurate knowledge of transcriptional regulatory elements. TRED (http://rulai.cshl.edu/TRED) was designed as a resource for gene regulation and function studies. It collects mammalian cis- and trans-regulatory elements together with experimental evidence. All the regulatory elements were mapped on to the assembled genomes. In this new release, we included a total of 36 TF families involved in cancer. Accordingly, the number of target promoters and genes for TF families has increased dramatically. There are 11 660 target genes (7479 in human, 2691 in mouse and 1490 in rat) and 14 908 target promoters (10 225 in human, 2985 in mouse and 1698 in rat). Additionally, we constructed GRNs for each TF family by connecting the TF-target gene pairs. Such interaction data between TFs and their target genes will assist detailed functional studies and help to obtain a panoramic view of the GRNs for cancer research.

UR - http://www.scopus.com/inward/record.url?scp=33846107777&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33846107777&partnerID=8YFLogxK

U2 - 10.1093/nar/gkl1041

DO - 10.1093/nar/gkl1041

M3 - Article

C2 - 17202159

AN - SCOPUS:33846107777

SN - 0305-1048

VL - 35

SP - D137-D140

JO - Nucleic acids research

JF - Nucleic acids research

IS - SUPPL. 1

ER -

TRED: A transcriptional regulatory element database, new entries and other development

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this