title: Comparative analysis of the transcriptome across distant species.
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.
authors.affiliation: 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 Computer Science, Yale University, 51 Prospect Street, New Haven, Connecticut 06511, USA [4] [5].
authors.forename: Mark B
authors.initials: MB
authors.lastname: Gerstein
authors.affiliation: 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].
authors.forename: Joel
authors.initials: J
authors.lastname: Rozowsky
authors.affiliation: 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].
authors.forename: Koon-Kiu
authors.initials: KK
authors.lastname: Yan
authors.affiliation: 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].
authors.forename: Daifeng
authors.initials: D
authors.lastname: Wang
authors.affiliation: 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].
authors.forename: Chao
authors.initials: C
authors.lastname: Cheng
authors.affiliation: 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].
authors.forename: James B
authors.initials: JB
authors.lastname: Brown
authors.affiliation: 1] Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA [2].
authors.forename: Carrie A
authors.initials: CA
authors.lastname: Davis
authors.affiliation: 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].
authors.forename: LaDeana
authors.initials: L
authors.lastname: Hillier
authors.affiliation: 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].
authors.forename: Cristina
authors.initials: C
authors.lastname: Sisu
authors.affiliation: 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 90095-7088, USA [4].
authors.forename: Jingyi Jessica
authors.initials: JJ
authors.lastname: Li
authors.affiliation: 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].
authors.forename: Baikang
authors.initials: B
authors.lastname: Pei
authors.affiliation: 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].
authors.forename: Arif O
authors.initials: AO
authors.lastname: Harmanci
authors.affiliation: 1] Department of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, Connecticut 06030, USA [2].
authors.forename: Michael O
authors.initials: MO
authors.lastname: Duff
authors.affiliation: 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].
authors.forename: Sarah
authors.initials: S
authors.lastname: Djebali
authors.affiliation: 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.
authors.forename: Roger P
authors.initials: RP
authors.lastname: Alexander
authors.affiliation: Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, Massachusetts 02115, USA.
authors.forename: Burak H
authors.initials: BH
authors.lastname: Alver
authors.affiliation: 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.
authors.forename: Raymond
authors.initials: R
authors.lastname: Auerbach
authors.affiliation: Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
authors.forename: Kimberly
authors.initials: K
authors.lastname: Bell
authors.affiliation: Department of Statistics, University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Bickel
authors.affiliation: 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.
authors.forename: Max E
authors.initials: ME
authors.lastname: Boeck
authors.affiliation: 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.
authors.forename: Nathan P
authors.initials: NP
authors.lastname: Boley
authors.affiliation: Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
authors.forename: Benjamin W
authors.initials: BW
authors.lastname: Booth
authors.affiliation: 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.
authors.forename: Lucy
authors.initials: L
authors.lastname: Cherbas
authors.affiliation: 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.
authors.forename: Peter
authors.initials: P
authors.lastname: Cherbas
authors.affiliation: MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Di
authors.affiliation: Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
authors.forename: Alex
authors.initials: A
authors.lastname: Dobin
authors.affiliation: Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
authors.forename: Jorg
authors.initials: J
authors.lastname: Drenkow
authors.affiliation: 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.
authors.forename: Brent
authors.initials: B
authors.lastname: Ewing
authors.affiliation: 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.
authors.forename: Gang
authors.initials: G
authors.lastname: Fang
authors.affiliation: Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
authors.forename: Megan
authors.initials: M
authors.lastname: Fastuca
authors.affiliation: National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA.
authors.forename: Elise A
authors.initials: EA
authors.lastname: Feingold
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Adam
authors.initials: A
authors.lastname: Frankish
authors.affiliation: MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Guanjun
authors.initials: G
authors.lastname: Gao
authors.affiliation: National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Good
authors.affiliation: 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.
authors.forename: Roderic
authors.initials: R
authors.lastname: Guigó
authors.affiliation: Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
authors.forename: Ann
authors.initials: A
authors.lastname: Hammonds
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Jen
authors.initials: J
authors.lastname: Harrow
authors.affiliation: Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
authors.forename: Roger A
authors.initials: RA
authors.lastname: Hoskins
authors.affiliation: 1] Center for Integrative Genomics, University of Lausanne, Genopode building, Lausanne 1015, Switzerland [2] Swiss Institute of Bioinformatics, Genopode building, Lausanne 1015, Switzerland.
authors.forename: Cédric
authors.initials: C
authors.lastname: Howald
authors.affiliation: MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Long
authors.initials: L
authors.lastname: Hu
authors.affiliation: Department of Statistics, University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA.
authors.forename: Haiyan
authors.initials: H
authors.lastname: Huang
authors.affiliation: 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.
authors.forename: Tim J P
authors.initials: TJ
authors.lastname: Hubbard
authors.affiliation: 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.
authors.forename: Chau
authors.initials: C
authors.lastname: Huynh
authors.affiliation: Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
authors.forename: Sonali
authors.initials: S
authors.lastname: Jha
authors.affiliation: Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520-8005, USA.
authors.forename: Dionna
authors.initials: D
authors.lastname: Kasper
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, PO Box 208103, Yale University, New Haven, Connecticut 06520, USA.
authors.forename: Masaomi
authors.initials: M
authors.lastname: Kato
authors.affiliation: Department of Biology, Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405-7005, USA.
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Kaufman
authors.affiliation: 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.
authors.forename: Robert R
authors.initials: RR
authors.lastname: Kitchen
authors.affiliation: Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, New York 10065, USA.
authors.forename: Erik
authors.initials: E
authors.lastname: Ladewig
authors.affiliation: 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.
authors.forename: Julien
authors.initials: J
authors.lastname: Lagarde
authors.affiliation: Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, New York 10065, USA.
authors.forename: Eric
authors.initials: E
authors.lastname: Lai
authors.affiliation: 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.
authors.forename: Jing
authors.initials: J
authors.lastname: Leng
authors.affiliation: MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Zhi
authors.initials: Z
authors.lastname: Lu
authors.affiliation: 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.
authors.forename: Michael
authors.initials: M
authors.lastname: MacCoss
authors.affiliation: 1] 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.
authors.forename: Gemma
authors.initials: G
authors.lastname: May
authors.affiliation: Department of Cell and Developmental Biology, Vanderbilt University, 465 21st Avenue South, Nashville, Tennessee 37232-8240, USA.
authors.forename: Rebecca
authors.initials: R
authors.lastname: McWhirter
authors.affiliation: 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.
authors.forename: Gennifer
authors.initials: G
authors.lastname: Merrihew
authors.affiliation: Department of Cell and Developmental Biology, Vanderbilt University, 465 21st Avenue South, Nashville, Tennessee 37232-8240, USA.
authors.forename: David M
authors.initials: DM
authors.lastname: Miller
authors.affiliation: 1] Developmental and Cell Biology, University of California, Irvine, California 92697, USA [2] Center for Complex Biological Systems, University of California, Irvine, California 92697, USA.
authors.forename: Ali
authors.initials: A
authors.lastname: Mortazavi
authors.affiliation: 1] Developmental and Cell Biology, University of California, Irvine, California 92697, USA [2] Center for Complex Biological Systems, University of California, Irvine, California 92697, USA.
authors.forename: Rabi
authors.initials: R
authors.lastname: Murad
authors.affiliation: Section 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.
authors.forename: Brian
authors.initials: B
authors.lastname: Oliver
authors.affiliation: Department of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, Connecticut 06030, USA.
authors.forename: Sara
authors.initials: S
authors.lastname: Olson
authors.affiliation: Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, Massachusetts 02115, USA.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Park
authors.affiliation: National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Pazin
authors.affiliation: 1] 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.
authors.forename: Norbert
authors.initials: N
authors.lastname: Perrimon
authors.affiliation: 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.
authors.forename: Dmitri
authors.initials: D
authors.lastname: Pervouchine
authors.affiliation: Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520-8005, USA.
authors.forename: Valerie
authors.initials: V
authors.lastname: Reinke
authors.affiliation: Center for Integrative Genomics, University of Lausanne, Genopode building, Lausanne 1015, Switzerland.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Reymond
authors.affiliation: Department of Statistics, University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA.
authors.forename: Garrett
authors.initials: G
authors.lastname: Robinson
authors.affiliation: 1] 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.
authors.forename: Anastasia
authors.initials: A
authors.lastname: Samsonova
authors.affiliation: 1] 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.
authors.forename: Gary I
authors.initials: GI
authors.lastname: Saunders
authors.affiliation: Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
authors.forename: Felix
authors.initials: F
authors.lastname: Schlesinger
authors.affiliation: 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.
authors.forename: Anurag
authors.initials: A
authors.lastname: Sethi
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, PO Box 208103, Yale University, New Haven, Connecticut 06520, USA.
authors.forename: Frank J
authors.initials: FJ
authors.lastname: Slack
authors.affiliation: Department of Cell and Developmental Biology, Vanderbilt University, 465 21st Avenue South, Nashville, Tennessee 37232-8240, USA.
authors.forename: William C
authors.initials: WC
authors.lastname: Spencer
authors.affiliation: 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.
authors.forename: Marcus H
authors.initials: MH
authors.lastname: Stoiber
authors.affiliation: 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.
authors.forename: Pnina
authors.initials: P
authors.lastname: Strasbourger
authors.affiliation: 1] 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.
authors.forename: Andrea
authors.initials: A
authors.lastname: Tanzer
authors.affiliation: 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.
authors.forename: Owen A
authors.initials: OA
authors.lastname: Thompson
authors.affiliation: Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Wan
authors.affiliation: Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520-8005, USA.
authors.forename: Guilin
authors.initials: G
authors.lastname: Wang
authors.affiliation: Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
authors.forename: Huaien
authors.initials: H
authors.lastname: Wang
authors.affiliation: Department of Cell and Developmental Biology, Vanderbilt University, 465 21st Avenue South, Nashville, Tennessee 37232-8240, USA.
authors.forename: Kathie L
authors.initials: KL
authors.lastname: Watkins
authors.affiliation: Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, New York 10065, USA.
authors.forename: Jiayu
authors.initials: J
authors.lastname: Wen
authors.affiliation: MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Kejia
authors.initials: K
authors.lastname: Wen
authors.affiliation: Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
authors.forename: Chenghai
authors.initials: C
authors.lastname: Xue
authors.affiliation: 1] 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.
authors.forename: Li
authors.initials: L
authors.lastname: Yang
authors.affiliation: 1] 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.
authors.forename: Kevin
authors.initials: K
authors.lastname: Yip
authors.affiliation: Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
authors.forename: Chris
authors.initials: C
authors.lastname: Zaleski
authors.affiliation: 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.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: 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.
authors.forename: Henry
authors.initials: H
authors.lastname: Zheng
authors.affiliation: 1] 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].
authors.forename: Steven E
authors.initials: SE
authors.lastname: Brenner
authors.affiliation: 1] Department of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, Connecticut 06030, USA [2].
authors.forename: Brenton R
authors.initials: BR
authors.lastname: Graveley
authors.affiliation: 1] Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA [2].
authors.forename: Susan E
authors.initials: SE
authors.lastname: Celniker
authors.affiliation: 1] Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA [2].
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Gingeras
authors.affiliation: 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].
authors.forename: Robert
authors.initials: R
authors.lastname: Waterston
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000196:embryology / Q000235:genetics* / Q000254:growth & development; D002843:Chromatin / Q000235:genetics; D016000:Cluster Analysis; D004331:Drosophila melanogaster / Q000235:genetics* / Q000254:growth & development; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental / Q000235:genetics; D006657:Histones / Q000378:metabolism; D006801:Humans; D007814:Larva / Q000235:genetics / Q000254:growth & development; D008957:Models, Genetic; D058977:Molecular Sequence Annotation; D011401:Promoter Regions, Genetic / Q000235:genetics; D011679:Pupa / Q000235:genetics / Q000254:growth & development; D022661:RNA, Untranslated / Q000235:genetics; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics*
chemical_list: D002843:Chromatin; D006657:Histones; D022661:RNA, Untranslated