Evidence map›Paper›PMID 25164755›Full record

ArticleNature2014

Comparative analysis of the transcriptome across distant species.

Mark B Gerstein, Joel Rozowsky, Koon-Kiu Yan, Daifeng Wang, Chao Cheng, James B Brown, Carrie A Davis, LaDeana Hillier, Cristina Sisu, Jingyi Jessica Li and 86 more

Abstract 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 173 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
173citing papers in PubMed, 2 pooled it
–field-weighted citation impact
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

173 citing papers in PubMed, 2 syntheses or guidelines pooled it.

  1. Pooled it
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113 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

96 authors.

Mark B Gerstein1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [3] Department of Computer Science, Yale University, 51 Prospect Street, New Haven, Connecticut 06511, USA [4] [5].
Joel Rozowsky1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [3].
Koon-Kiu Yan1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [3].
Daifeng Wang1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [3].
Chao Cheng1] Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA [2] Institute for Quantitative Biomedical Sciences, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire 03766, USA [3].
James B Brown1] Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA [2] Department of Statistics, University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA [3].
Carrie A Davis1] Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA [2].
LaDeana Hillier1] Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA [2].
Cristina Sisu1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [3].
Jingyi Jessica Li1] Department of Statistics, University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA [2] Department of Statistics, University of California, Los Angeles, California 90095-1554, USA [3] Department of Human Genetics, University of California, Los Angeles, California 90095-7088, USA [4].
Baikang Pei1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [3].
Arif O Harmanci1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [3].
Michael O Duff1] Department of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, Connecticut 06030, USA [2].
Sarah Djebali1] Centre for Genomic Regulation, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain [2] Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain [3].
Roger P Alexander1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA.
Burak H AlverCenter for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, Massachusetts 02115, USA.
Raymond Auerbach1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA.
Kimberly BellFunctional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
Peter J BickelDepartment of Statistics, University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA.
Max E BoeckDepartment of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA.
Nathan P Boley1] Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA [2] Department of Biostatistics, University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA.
Benjamin W BoothDepartment of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
Lucy Cherbas1] Department of Biology, Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405-7005, USA [2] Center for Genomics and Bioinformatics, Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405-7005, USA.
Peter Cherbas1] Department of Biology, Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405-7005, USA [2] Center for Genomics and Bioinformatics, Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405-7005, USA.
Chao DiMOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.
Alex DobinFunctional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
Jorg DrenkowFunctional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
Brent EwingDepartment of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA.
Gang Fang1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA.
Megan FastucaFunctional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
Elise A FeingoldNational Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA.
Adam FrankishWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Guanjun GaoMOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.
Peter J GoodNational Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA.
Roderic Guigó1] Centre for Genomic Regulation, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain [2] Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain.
Ann HammondsDepartment of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
Jen HarrowWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Roger A HoskinsDepartment of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
Cédric Howald1] Center for Integrative Genomics, University of Lausanne, Genopode building, Lausanne 1015, Switzerland [2] Swiss Institute of Bioinformatics, Genopode building, Lausanne 1015, Switzerland.
Long HuMOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.
Haiyan HuangDepartment of Statistics, University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA.
Tim J P Hubbard1] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK [2] Medical and Molecular Genetics, King's College London, London WC2R 2LS, UK.
Chau HuynhDepartment of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA.
Sonali JhaFunctional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
Dionna KasperDepartment of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520-8005, USA.
Masaomi KatoDepartment of Molecular, Cellular and Developmental Biology, PO Box 208103, Yale University, New Haven, Connecticut 06520, USA.
Thomas C KaufmanDepartment of Biology, Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405-7005, USA.
Robert R Kitchen1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA.
Erik LadewigSloan-Kettering Institute, 1275 York Avenue, Box 252, New York, New York 10065, USA.
Julien Lagarde1] Centre for Genomic Regulation, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain [2] Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain.
Eric LaiSloan-Kettering Institute, 1275 York Avenue, Box 252, New York, New York 10065, USA.
Jing Leng1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA.
Zhi LuMOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.
Michael MacCossDepartment of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA.
Gemma May1] Department of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, Connecticut 06030, USA [2] Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 USA.
Rebecca McWhirterDepartment of Cell and Developmental Biology, Vanderbilt University, 465 21st Avenue South, Nashville, Tennessee 37232-8240, USA.
Gennifer MerrihewDepartment of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA.
David M MillerDepartment of Cell and Developmental Biology, Vanderbilt University, 465 21st Avenue South, Nashville, Tennessee 37232-8240, USA.
Ali Mortazavi1] Developmental and Cell Biology, University of California, Irvine, California 92697, USA [2] Center for Complex Biological Systems, University of California, Irvine, California 92697, USA.
Rabi Murad1] Developmental and Cell Biology, University of California, Irvine, California 92697, USA [2] Center for Complex Biological Systems, University of California, Irvine, California 92697, USA.
Brian OliverSection of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
Sara OlsonDepartment of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, Connecticut 06030, USA.
Peter J ParkCenter for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, Massachusetts 02115, USA.
Michael J PazinNational Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA.
Norbert Perrimon1] Department of Genetics and Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA [2] Howard Hughes Medical Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA.
Dmitri Pervouchine1] Centre for Genomic Regulation, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain [2] Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain.
Valerie ReinkeDepartment of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520-8005, USA.
Alexandre ReymondCenter for Integrative Genomics, University of Lausanne, Genopode building, Lausanne 1015, Switzerland.
Garrett RobinsonDepartment of Statistics, University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA.
Anastasia Samsonova1] Department of Genetics and Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA [2] Howard Hughes Medical Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA.
Gary I Saunders1] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK [2] European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
Felix SchlesingerFunctional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
Anurag Sethi1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA.
Frank J SlackDepartment of Molecular, Cellular and Developmental Biology, PO Box 208103, Yale University, New Haven, Connecticut 06520, USA.
William C SpencerDepartment of Cell and Developmental Biology, Vanderbilt University, 465 21st Avenue South, Nashville, Tennessee 37232-8240, USA.
Marcus H Stoiber1] Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA [2] Department of Biostatistics, University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA.
Pnina StrasbourgerDepartment of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA.
Andrea Tanzer1] Bioinformatics and Genomics Programme, Center for Genomic Regulation, Universitat Pompeu Fabra (CRG-UPF), 08003 Barcelona, Catalonia, Spain [2] Institute for Theoretical Chemistry, Theoretical Biochemistry Group (TBI), University of Vienna, Währingerstrasse 17/3/303, A-1090 Vienna, Austria.
Owen A ThompsonDepartment of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA.
Kenneth H WanDepartment of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
Guilin WangDepartment of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520-8005, USA.
Huaien WangFunctional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
Kathie L WatkinsDepartment of Cell and Developmental Biology, Vanderbilt University, 465 21st Avenue South, Nashville, Tennessee 37232-8240, USA.
Jiayu WenSloan-Kettering Institute, 1275 York Avenue, Box 252, New York, New York 10065, USA.
Kejia WenMOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.
Chenghai XueFunctional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
Li Yang1] Department of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, Connecticut 06030, USA [2] Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
Kevin Yip1] Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong [2] 5 CUHK-BGI Innovation Institute of Trans-omics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
Chris ZaleskiFunctional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
Yan Zhang1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA.
Henry Zheng1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, 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 [3].
Brenton R Graveley1] Department of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, Connecticut 06030, USA [2].
Susan E Celniker1] Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA [2].
Thomas R Gingeras1] Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA [2].
Robert Waterston1] Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA [2].

Funding

X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI Nicholas D Socci · 1985 to 2026
$347.4M
Single-Cell Biology Shared ResourceP30CA045508 · NCI · COLD SPRING HARBOR LABORATORY · PI John Edward Moses · 1987 to 2026
$118.9M
Drosophila Functional GenomicsZIADK015600 · NIDDK · NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES · PI OLIVER, BRIAN · 2009 to 2025
$23.9M
MEDICAL INFORMATICS RESEARCH TRAINING AT YALET15LM007056 · NLM · YALE UNIVERSITY · PI Mark Bender Gerstein, LUCILA OHNO-MACHADO · 1987 to 2026
$22.2M
Resource ProjectU41HG007355 · NHGRI · UNIVERSITY OF WASHINGTON · PI WATERSTON, ROBERT H · 2013 to 2021
$20.8M
GENCODE Resource ProjectU41HG007234 · NHGRI · SANGER INSTITUTE · PI FLICEK, PAUL · 2013 to 2020
$20.3M
Comprehensive characterization of the Drosophila transcriptomeU01HG004271 · NHGRI · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI CELNIKER, SUSAN E · 2007 to 2011
$18.4M
Comprhensive analysis of functional RNA elements encoded in the human genomeU54HG007005 · NHGRI · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI GRAVELEY, BRENTON R. · 2012 to 2017
$12.5M
Integrated human genome annotation: generation of a reference gene setU54HG004555 · NHGRI · SANGER INSTITUTE · PI HUBBARD, TIMOTHY JOHN · 2007 to 2012
$11.2M
Landscape of transcription in human and mouseU54HG007004 · NHGRI · COLD SPRING HARBOR LABORATORY · PI GINGERAS, THOMAS RAYMOND · 2012 to 2017
$10.6M
EDAC: ENCODE Data Analysis CenterU41HG007000 · NHGRI · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI WENG, ZHIPING · 2012 to 2016
$9.8M
Genome-Wide Mapping of Chromosomal Proteins in DrosophiliaU01HG004258 · NHGRI · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI KARPEN, GARY H · 2007 to 2011
$9.6M
Howard Hughes Medical InstituteIntramural NIH HHS ZIA DK015600NCI NIH HHS P30 CA008748NCI NIH HHS P30 CA045508NHGRI NIH HHS 1U01HG007031-01NHGRI NIH HHS 5U01HG004695-04NHGRI NIH HHS 5U54HG004555NHGRI NIH HHS HG007000NHGRI NIH HHS HG007355NHGRI NIH HHS K99 HG006698NHGRI NIH HHS RC2 HG005639NHGRI NIH HHS RC2-HG005639NHGRI NIH HHS U01 HG004258NHGRI NIH HHS U01HG004258NHGRI NIH HHS U01 HG004261NHGRI NIH HHS U01-HG004261NHGRI NIH HHS U01 HG 004263NHGRI NIH HHS U01 HG004271NHGRI NIH HHS U01 HG004695NHGRI NIH HHS U01 HG007031NHGRI NIH HHS U41 HG007000NHGRI NIH HHS U41 HG007234NHGRI NIH HHS U41 HG007355NHGRI NIH HHS U54 HG004555NHGRI NIH HHS U54 HG006944NHGRI NIH HHS U54 HG006994NHGRI NIH HHS U54 HG007004NHGRI NIH HHS U54 HG007005NHGRI NIH HHS U54HG007005NICHD NIH HHS T32 HD060555NIGMS NIH HHS R01 GM076655NLM NIH HHS T15 LM007056Wellcome TrustWellcome Trust WT098051
6 · The paper itself

Abstract

The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features. Specifically, we discover co-expression modules shared across animals, many of which are enriched in developmental genes. Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair. Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a 'universal model' based on a single set of organism-independent parameters.

Indexed as

Gene Expression ProfilingAnimalsCaenorhabditis elegansChromatinCluster AnalysisDrosophila melanogasterGene Expression Regulation, DevelopmentalHistonesHumansLarvaModels, GeneticMolecular Sequence AnnotationPromoter Regions, GeneticPupaRNA, UntranslatedSequence Analysis, RNAChromatinHistonesRNA, Untranslated

Identifiers

PMID25164755
PMCPMC4155737

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