CLARE: Cracking the LAnguage of Regulatory Elements

Leila Taher; Leelavati Narlikar; Ivan Ovcharenko

doi:10.1093/bioinformatics/btr704

CLARE: Cracking the LAnguage of Regulatory Elements

Leila Taher, Leelavati Narlikar, Ivan Ovcharenko

Institute of Biomedical Informatics (7200)

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

Abstract

UNLABELLED: CLARE is a computational method designed to reveal sequence encryption of tissue-specific regulatory elements. Starting with a set of regulatory elements known to be active in a particular tissue/process, it learns the sequence code of the input set and builds a predictive model from features specific to those elements. The resulting model can then be applied to user-supplied genomic regions to identify novel candidate regulatory elements. CLARE's model also provides a detailed analysis of transcription factors that most likely bind to the elements, making it an invaluable tool for understanding mechanisms of tissue-specific gene regulation.

AVAILABILITY: CLARE is freely accessible at http://clare.dcode.org/.

Original language	English
Pages (from-to)	581-3
Number of pages	3
Journal	Bioinformatics
Volume	28
Issue number	4
DOIs	https://doi.org/10.1093/bioinformatics/btr704
Publication status	Published - 15 Feb 2012

Keywords

Animals
Enhancer Elements, Genetic
Gene Expression Regulation
Genomics
Humans
Mice
Organ Specificity
Prosencephalon/metabolism
Regulatory Sequences, Nucleic Acid
Software
Transcription Factors/metabolism

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10.1093/bioinformatics/btr704

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title = "CLARE: Cracking the LAnguage of Regulatory Elements",

abstract = "UNLABELLED: CLARE is a computational method designed to reveal sequence encryption of tissue-specific regulatory elements. Starting with a set of regulatory elements known to be active in a particular tissue/process, it learns the sequence code of the input set and builds a predictive model from features specific to those elements. The resulting model can then be applied to user-supplied genomic regions to identify novel candidate regulatory elements. CLARE's model also provides a detailed analysis of transcription factors that most likely bind to the elements, making it an invaluable tool for understanding mechanisms of tissue-specific gene regulation.AVAILABILITY: CLARE is freely accessible at http://clare.dcode.org/.",

keywords = "Animals, Enhancer Elements, Genetic, Gene Expression Regulation, Genomics, Humans, Mice, Organ Specificity, Prosencephalon/metabolism, Regulatory Sequences, Nucleic Acid, Software, Transcription Factors/metabolism",

author = "Leila Taher and Leelavati Narlikar and Ivan Ovcharenko",

year = "2012",

month = feb,

day = "15",

doi = "10.1093/bioinformatics/btr704",

language = "English",

volume = "28",

pages = "581--3",

journal = "Bioinformatics",

issn = "1367-4803",

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TY - JOUR

T1 - CLARE

T2 - Cracking the LAnguage of Regulatory Elements

AU - Taher, Leila

AU - Narlikar, Leelavati

AU - Ovcharenko, Ivan

PY - 2012/2/15

Y1 - 2012/2/15

N2 - UNLABELLED: CLARE is a computational method designed to reveal sequence encryption of tissue-specific regulatory elements. Starting with a set of regulatory elements known to be active in a particular tissue/process, it learns the sequence code of the input set and builds a predictive model from features specific to those elements. The resulting model can then be applied to user-supplied genomic regions to identify novel candidate regulatory elements. CLARE's model also provides a detailed analysis of transcription factors that most likely bind to the elements, making it an invaluable tool for understanding mechanisms of tissue-specific gene regulation.AVAILABILITY: CLARE is freely accessible at http://clare.dcode.org/.

AB - UNLABELLED: CLARE is a computational method designed to reveal sequence encryption of tissue-specific regulatory elements. Starting with a set of regulatory elements known to be active in a particular tissue/process, it learns the sequence code of the input set and builds a predictive model from features specific to those elements. The resulting model can then be applied to user-supplied genomic regions to identify novel candidate regulatory elements. CLARE's model also provides a detailed analysis of transcription factors that most likely bind to the elements, making it an invaluable tool for understanding mechanisms of tissue-specific gene regulation.AVAILABILITY: CLARE is freely accessible at http://clare.dcode.org/.

KW - Animals

KW - Enhancer Elements, Genetic

KW - Gene Expression Regulation

KW - Genomics

KW - Humans

KW - Mice

KW - Organ Specificity

KW - Prosencephalon/metabolism

KW - Regulatory Sequences, Nucleic Acid

KW - Software

KW - Transcription Factors/metabolism

U2 - 10.1093/bioinformatics/btr704

DO - 10.1093/bioinformatics/btr704

M3 - Article

C2 - 22199387

SN - 1367-4803

VL - 28

SP - 581

EP - 583

JO - Bioinformatics

JF - Bioinformatics

IS - 4

ER -

CLARE: Cracking the LAnguage of Regulatory Elements

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Keywords

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