Evidence map›Paper›PMID 25164757›Full record

ArticleNature2014

Comparative analysis of regulatory information and circuits across distant species.

Alan P Boyle, Carlos L Araya, Cathleen Brdlik, Philip Cayting, Chao Cheng, Yong Cheng, Kathryn Gardner, LaDeana W Hillier, Judith Janette, Lixia Jiang and 30 more

Open access · hybridAbstract readComparative Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 109 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
109citing papers in PubMed, 1 pooled it
14.5field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

109 citing papers in PubMed, 1 synthesis or guideline pooled it, 230 citations in OpenAlex.

  1. Pooled it
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  20. Analysis of theCell genomics · 2023
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49 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

40 authors at 8 institutions in 1 country.

Alan P Boyle1] Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA [2].
Carlos L Araya1] Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA [2].
Cathleen BrdlikDepartment of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.
Philip CaytingDepartment of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.
Chao ChengProgram of Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA.
Yong ChengDepartment of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.
Kathryn GardnerDepartment of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA.
LaDeana W HillierDepartment of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
Judith JanetteDepartment of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA.
Lixia JiangDepartment of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.
Dionna KasperDepartment of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA.
Trupti KawliDepartment of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.
Pouya KheradpourComputer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
Anshul Kundaje1] Department of Computer Science, Stanford University, Stanford, California 94305, USA [2] Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
Jingyi Jessica Li1] Department of Statistics, University of California, Berkeley, California 94720, USA [2] Department of Statistics, University of California, Los Angeles, California 90095, USA.
Lijia MaDepartment of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
Wei NiuDepartment of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA.
E Jay RehmInstitute for Genomics and Systems Biology, University of Chicago, Chicago, Ilinois 60637, USA.
Joel RozowskyProgram of Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA.
Matthew SlatteryInstitute for Genomics and Systems Biology, University of Chicago, Chicago, Ilinois 60637, USA.
Rebecca SpokonyInstitute for Genomics and Systems Biology, University of Chicago, Chicago, Ilinois 60637, USA.
Robert TerrellDepartment of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
Dionne VafeadosDepartment of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
Daifeng WangProgram of Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA.
Peter WeisdeppDepartment of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
Yi-Chieh WuComputer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
Dan XieDepartment of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.
Koon-Kiu YanProgram of Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA.
Elise A FeingoldNational Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, 20892, USA.
Peter J GoodNational Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, 20892, USA.
Michael J PazinNational Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, 20892, USA.
Haiyan HuangDepartment of Statistics, University of California, Berkeley, California 94720, USA.
Peter J BickelDepartment of Statistics, University of California, Berkeley, California 94720, USA.
Steven E Brenner1] Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA [2] Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.
Valerie ReinkeDepartment of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA.
Robert H WaterstonDepartment of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
Mark GersteinProgram of Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA.
Kevin P WhiteInstitute for Genomics and Systems Biology, University of Chicago, Chicago, Ilinois 60637, USA.
Manolis KellisComputer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
Michael SnyderDepartment of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.
Stanford University · USYale University · USUniversity of Washington · USUniversity of California, Berkeley · USUniversity of Chicago · USMassachusetts Institute of Technology · USNational Human Genome Research Institute · USNational Institutes of Health · US

Funding

Re-Engineering Translational Research at the University of ChicagoUL1TR000430 · NCATS · UNIVERSITY OF CHICAGO · PI SOLWAY, JULIAN · 2012 to 2016
$20.2M
CORE: ADMINISTRATIVEP50GM081892 · NIGMS · UNIVERSITY OF CHICAGO · PI WHITE, KEVIN P. · 2008 to 2013
$15.9M
Production Center for Global Mapping of Regulatory ElementsU54HG004558 · NHGRI · YALE UNIVERSITY · PI SNYDER, MICHAEL P. · 2007 to 2011
$15.4M
Production Center for Mapping Regulatory Regions of the Human GenomeU54HG006996 · NHGRI · STANFORD UNIVERSITY · PI SNYDER, MICHAEL P. · 2012 to 2016
$14.6M
A Cis Regulatory map of the Drosophila GenomeU01HG004264 · NHGRI · UNIVERSITY OF CHICAGO · PI WHITE, KEVIN P. · 2007 to 2011
$12.1M
Global Identification of Transcription Factor Binding Sites in C. elegansU01HG004267 · NHGRI · YALE UNIVERSITY · PI SNYDER, MICHAEL P. · 2007 to 2011
$8.1M
Regulatory Morif Discovery in the Human Genome Using Comparative GenomicsR01HG004037 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI KELLIS, MANOLIS · 2007 to 2015
$3.9M
Enhancing ENCODE Through a Transcription Factor Tagging Approach to ChIP-seqRC2HG005679 · NHGRI · UNIVERSITY OF CHICAGO · PI WHITE, KEVIN P. · 2009 to 2011
$2.7M
Global Discovery and Validation of Functional Regulatory ElementsK99HG007356 · NHGRI · STANFORD UNIVERSITY · PI BOYLE, ALAN P · 2013 to 2013
$94k
Investigating Rb/E2F control over gene expression during germline differentiationF32GM101778 · NIGMS · YALE UNIVERSITY · PI GARDNER, KATHRYN ELIZABETH · 2012 to 2013
$90k
NCATS NIH HHS UL1 TR000430NHGRI NIH HHS K99 HG007356NHGRI NIH HHS R01 HG004037NHGRI NIH HHS RC2 HG005679NHGRI NIH HHS U01 HG004264NHGRI NIH HHS U01 HG004267NHGRI NIH HHS U54 HG004558NHGRI NIH HHS U54 HG006996NIGMS NIH HHS F32 GM101778NIGMS NIH HHS P50 GM081892
6 · The paper itself

Abstract

Despite the large evolutionary distances between metazoan species, they can show remarkable commonalities in their biology, and this has helped to establish fly and worm as model organisms for human biology. Although studies of individual elements and factors have explored similarities in gene regulation, a large-scale comparative analysis of basic principles of transcriptional regulatory features is lacking. Here we map the genome-wide binding locations of 165 human, 93 worm and 52 fly transcription regulatory factors, generating a total of 1,019 data sets from diverse cell types, developmental stages, or conditions in the three species, of which 498 (48.9%) are presented here for the first time. We find that structural properties of regulatory networks are remarkably conserved and that orthologous regulatory factor families recognize similar binding motifs in vivo and show some similar co-associations. Our results suggest that gene-regulatory properties previously observed for individual factors are general principles of metazoan regulation that are remarkably well-preserved despite extensive functional divergence of individual network connections. The comparative maps of regulatory circuitry provided here will drive an improved understanding of the regulatory underpinnings of model organism biology and how these relate to human biology, development and disease.

Indexed as

Evolution, MolecularAnimalsBinding SitesCaenorhabditis elegansChromatin ImmunoprecipitationConserved SequenceDrosophila melanogasterGene Expression RegulationGene Expression Regulation, DevelopmentalGene Regulatory NetworksGenomeHumansMolecular Sequence AnnotationNucleotide MotifsOrgan SpecificityTranscription FactorsTranscription Factors

Identifiers

PMID25164757
PMCPMC4336544
OpenAlexW2095150428

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.