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Comparative analysis of the transcriptome across distant species.
Gerstein, Mark B; Rozowsky, Joel; Yan, Koon-Kiu; Wang, Daifeng; Cheng, Chao; Brown, James B; Davis, Carrie A; Hillier, LaDeana; Sisu, Cristina; Li, Jingyi Jessica; Pei, Baikang; Harmanci, Arif O; Duff, Michael O; Djebali, Sarah; Alexander, Roger P; Alver, Burak H; Auerbach, Raymond; Bell, Kimberly; Bickel, Peter J; Boeck, Max E; Boley, Nathan P; Booth, Benjamin W; Cherbas, Lucy; Cherbas, Peter; Di, Chao; Dobin, Alex; Drenkow, Jorg; Ewing, Brent; Fang, Gang; Fastuca, Megan; Feingold, Elise A; Frankish, Adam; Gao, Guanjun; Good, Peter J; Guigó, Roderic; Hammonds, Ann; Harrow, Jen; Hoskins, Roger A; Howald, Cédric; Hu, Long; Huang, Haiyan; Hubbard, Tim J P; Huynh, Chau; Jha, Sonali; Kasper, Dionna; Kato, Masaomi; Kaufman, Thomas C; Kitchen, Robert R; Ladewig, Erik; Lagarde, Julien.
Afiliação
  • Gerstein MB; 1] 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 Compute
  • Rozowsky J; 1] 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].
  • Yan KK; 1] 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].
  • Wang D; 1] 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].
  • Cheng C; 1] 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].
  • Brown JB; 1] 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].
  • Davis CA; 1] Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA [2].
  • Hillier L; 1] 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].
  • Sisu C; 1] 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].
  • Li JJ; 1] 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 90
  • Pei B; 1] 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].
  • Harmanci AO; 1] 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].
  • Duff MO; 1] Department of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, Connecticut 06030, USA [2].
  • Djebali S; 1] 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].
  • Alexander RP; 1] 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.
  • Alver BH; Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, Massachusetts 02115, USA.
  • Auerbach R; 1] 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.
  • Bell K; Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
  • Bickel PJ; Department of Statistics, University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA.
  • Boeck ME; 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.
  • Boley NP; 1] 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.
  • Booth BW; Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
  • Cherbas L; 1] 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.
  • Cherbas P; 1] 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.
  • Di C; MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.
  • Dobin A; Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
  • Drenkow J; Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
  • Ewing B; 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.
  • Fang G; 1] 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.
  • Fastuca M; Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
  • Feingold EA; National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA.
  • Frankish A; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
  • Gao G; MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.
  • Good PJ; National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA.
  • Guigó R; 1] 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.
  • Hammonds A; Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
  • Harrow J; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
  • Hoskins RA; Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
  • Howald C; 1] Center for Integrative Genomics, University of Lausanne, Genopode building, Lausanne 1015, Switzerland [2] Swiss Institute of Bioinformatics, Genopode building, Lausanne 1015, Switzerland.
  • Hu L; MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.
  • Huang H; Department of Statistics, University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA.
  • Hubbard TJ; 1] 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.
  • Huynh C; 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.
  • Jha S; Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
  • Kasper D; Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520-8005, USA.
  • Kato M; Department of Molecular, Cellular and Developmental Biology, PO Box 208103, Yale University, New Haven, Connecticut 06520, USA.
  • Kaufman TC; Department of Biology, Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405-7005, USA.
  • Kitchen RR; 1] 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.
  • Ladewig E; Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, New York 10065, USA.
  • Lagarde J; 1] 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.
Nature ; 512(7515): 445-8, 2014 Aug 28.
Article em En | MEDLINE | ID: mdl-25164755
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.
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Texto completo: 1 Bases de dados: MEDLINE Assunto principal: Caenorhabditis elegans / Perfilação da Expressão Gênica / Drosophila melanogaster / Transcriptoma Tipo de estudo: Prognostic_studies Limite: Animals / Humans Idioma: En Revista: Nature Ano de publicação: 2014 Tipo de documento: Article
Texto completo
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Texto completo: 1 Bases de dados: MEDLINE Assunto principal: Caenorhabditis elegans / Perfilação da Expressão Gênica / Drosophila melanogaster / Transcriptoma Tipo de estudo: Prognostic_studies Limite: Animals / Humans Idioma: En Revista: Nature Ano de publicação: 2014 Tipo de documento: Article