ArticleGenome research2014
Comparative validation of the D. melanogaster modENCODE transcriptome annotation.
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Article in Genome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 127 papers.
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127citing papers in PubMed
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Who cites it
127 citing papers in PubMed.
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- Paramutation-Like Behavior of Genic piRNA-Producing Loci inInternational journal of molecular sciences · 2025Article
- An orphan gene is essential for efficient sperm entry into eggs in Drosophila melanogaster.Genetics · 2025Article
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67 more citing papers are in PubMed but not listed here.
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Authors and funding
63 authors.
Zhen-Xia ChenNational Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA;
David SturgillNational Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA;
Jiaxin QuHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
Huaiyang JiangHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
Soo ParkDepartment of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
Nathan BoleyDepartment of Statistics, University of California, Berkeley, California 94720, USA;
Ana Maria SuzukiTechnology Development Group, RIKEN Omics Science Center and RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama City, Kanagawa, Japan 230-0045;
Anthony R FletcherDivision of Computational Bioscience, Center For Information Technology, National Institutes of Health, Bethesda, Maryland 20814, USA;
David C PlachetzkiDepartment of Evolution and Ecology, University of California, Davis, California 95616, USA;
Peter C FitzGeraldNational Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
Carlo G ArtieriNational Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA;
Joel AtallahDepartment of Evolution and Ecology, University of California, Davis, California 95616, USA;
Olga BarminaDepartment of Evolution and Ecology, University of California, Davis, California 95616, USA;
James B BrownDepartment of Statistics, University of California, Berkeley, California 94720, USA;
Kerstin P BlankenburgHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
Emily CloughNational Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA;
Abhijit DasguptaClinical Trials and Outcomes Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA;
Sai GubbalaHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
Yi HanHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
Joy C JayaseelanHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
Divya KalraHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
Yoo-Ah KimNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892, USA;
Christie L KovarHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
Sandra L LeeHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
Mingmei LiHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
James D MalleyDivision of Computational Bioscience, Center For Information Technology, National Institutes of Health, Bethesda, Maryland 20814, USA;
John H MaloneNational Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA;
Tittu MathewHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
Nicolas R MattiuzzoNational Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA;
Mala MunidasaHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
Donna M MuznyHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
Fiona OngeriHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
Lora PeralesHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
Teresa M PrzytyckaNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892, USA;
Ling-Ling PuHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
Garrett RobinsonDepartment of Statistics, University of California, Berkeley, California 94720, USA;
Rebecca L ThorntonHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
Nehad SaadaHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
Steven E SchererHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
Harold E SmithNational Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA;
Charles VinsonNational Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
Crystal B WarnerHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
Kim C WorleyHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
Yuan-Qing WuHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
Xiaoyan ZouHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
Peter CherbasDepartment of Biology, Indiana University, Bloomington, Indiana 47405, USA;
Manolis KellisComputer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 20139, USA;
Michael B EisenMolecular and Cell Biology, University of California, Berkeley, California 94720, USA;
Fabio PianoDepartment of Biology, New York University, New York, New York 10003, USA;
Karin KionteDepartment of Biology, New York University, New York, New York 10003, USA;
David H FitchDepartment of Biology, New York University, New York, New York 10003, USA;
Paul W SternbergHHMI and Division of Biology, California Institute of Technology, Pasadena, California 91125, USA;
Asher D CutterDepartment of Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, Canada;
Michael O DuffDepartment of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030-6403, USA.
Roger A HoskinsDepartment of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
Brenton R GraveleyDepartment of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030-6403, USA.
Richard A GibbsHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
Peter J BickelDepartment of Statistics, University of California, Berkeley, California 94720, USA;
Artyom KoppDepartment of Evolution and Ecology, University of California, Davis, California 95616, USA;
Piero CarninciTechnology Development Group, RIKEN Omics Science Center and RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama City, Kanagawa, Japan 230-0045;
Susan E CelnikerDepartment of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
Brian OliverNational Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA;
Stephen RichardsHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
Funding
The Human Genome Sequencing CenterU54HG003273 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI GIBBS, RICHARD A · 2004 to 2015
$341.3MCCR Collaborative Bioinformatics ResourceZICBC011532 · NCI · DIVISION OF BASIC SCIENCES - NCI · PI MALIK, MARIAM · 2013 to 2025
$33.7MCombinatorial and graph theoretical approach to systems biology and mol. evo.ZIALM200887 · NLM · NATIONAL LIBRARY OF MEDICINE · PI PRZYTYCKA, TERESA · 2009 to 2025
$24.4MDrosophila Functional GenomicsZIADK015600 · NIDDK · NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES · PI OLIVER, BRIAN · 2009 to 2025
$23.9MGenomics Core FacilityZICDK071001 · NIDDK · NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES · PI HANOVER, JOHN A. · 2009 to 2023
$16.6MRegulatory Morif Discovery in the Human Genome Using Comparative GenomicsR01HG004037 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI KELLIS, MANOLIS · 2007 to 2015
$3.9MStatistical Learning for Biomedical DataZIACT000271 · CIT · CENTER FOR INFORMATION TECHNOLOGY · PI MALLEY, JAMES D · 2009 to 2017
$1.2MArchitecture of a Genetic Network Governing MorphogenesisR01GM100140 · NIGMS · NEW YORK UNIVERSITY · PI FITCH, DAVID H. A. · 2012 to 2015
$1.1MGERMLINE SEX DETERMINATIONZ01DK015600 · NIDDK · NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES · PI OLIVER, BRIAN C · 1996 to 2008
$949kIntramural NIH HHS Z01 DK015600Intramural NIH HHS ZIA DK015600NHGRI NIH HHS R01 HG004037NHGRI NIH HHS U54 HG003273NHLBI NIH HHS U01HB004271NIDDK NIH HHS DK015600-18NIGMS NIH HHS R01 GM100140PHS HHS 1R0IGM082843
Abstract
Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species. For comparative transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species, and we performed cap analysis of gene expression in D. melanogaster and D. pseudoobscura. We also describe conservation of four distinct core promoter structures composed of combinations of elements at three positions. Overall, each type of genomic feature shows a characteristic divergence rate relative to neutral models, highlighting the value of multispecies alignment in annotating a target genome that should prove useful in the annotation of other high priority genomes, especially human and other mammalian genomes that are rich in noncoding sequences. We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community.
Indexed as
Gene Expression ProfilingMolecular Sequence AnnotationTranscriptomeAnimalsCluster AnalysisComputational BiologyDrosophila melanogasterEvolution, MolecularExonsFemaleGenome, InsectHumansMaleNucleotide MotifsPhylogenyPosition-Specific Scoring MatricesRNA Splice Sites
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