{"doi":"10.1101/gr.159384.113","title":"Comparative validation of the <i>D. melanogaster</i> modENCODE transcriptome annotation","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.","journal":"Genome Research","year":2014,"id":5158,"datarank":4.641108910386911,"base_score":5.262690188904886,"endowment":5.262690188904886,"self_citation_contribution":0.7894035283357329,"citation_network_contribution":3.851705382051178,"self_endowment_contribution":0.7894035283357329,"citer_contribution":3.851705382051178,"corpus_percentile":95.33534462752378,"corpus_rank":604,"citation_count":192,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.7487,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2014-07-01","fair_score":44.5833,"fair_percentile":32.89183222958057,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":45067,"name":"David Sturgill","orcid":"0000-0002-7902-3605","position":1,"is_corresponding":false},{"id":52113,"name":"Jiaxin Qu","orcid":"0000-0002-1122-9391","position":2,"is_corresponding":false},{"id":20069,"name":"Huaiyang Jiang","orcid":null,"position":3,"is_corresponding":false},{"id":52114,"name":"Soo Park","orcid":null,"position":4,"is_corresponding":false},{"id":17024,"name":"Nathan Boley","orcid":"0000-0001-7114-2450","position":5,"is_corresponding":false},{"id":11775,"name":"Ana Maria Suzuki","orcid":null,"position":6,"is_corresponding":false},{"id":52115,"name":"Anthony R. Fletcher","orcid":null,"position":7,"is_corresponding":false},{"id":52116,"name":"David C. Plachetzki","orcid":"0000-0002-6255-7117","position":8,"is_corresponding":false},{"id":52117,"name":"Peter C. FitzGerald","orcid":null,"position":9,"is_corresponding":false},{"id":45133,"name":"Carlo G. Artieri","orcid":null,"position":10,"is_corresponding":false},{"id":52118,"name":"Joel Atallah","orcid":"0000-0003-2425-2395","position":11,"is_corresponding":false},{"id":52119,"name":"Olga Barmina","orcid":"0000-0002-2297-4362","position":12,"is_corresponding":false},{"id":362,"name":"James B Brown","orcid":"0000-0002-5898-5848","position":13,"is_corresponding":false},{"id":52120,"name":"Kerstin P. Blankenburg","orcid":null,"position":14,"is_corresponding":false},{"id":52121,"name":"Emily Clough","orcid":"0009-0003-7602-1369","position":15,"is_corresponding":false},{"id":52122,"name":"Abhijit Dasgupta","orcid":"0000-0001-6062-9896","position":16,"is_corresponding":false},{"id":52123,"name":"Sai Gubbala","orcid":null,"position":17,"is_corresponding":false},{"id":52124,"name":"Yi Han","orcid":"0000-0001-7605-8979","position":18,"is_corresponding":false},{"id":14093,"name":"Jonathan R. Stretch","orcid":"0000-0002-2556-2005","position":19,"is_corresponding":false},{"id":2123,"name":"Richard Durbin","orcid":"0000-0002-9130-1006","position":20,"is_corresponding":false},{"id":52126,"name":"Yoo-Ah Kim","orcid":null,"position":21,"is_corresponding":false},{"id":19838,"name":"Doyle V. Ward","orcid":"0000-0002-4952-824X","position":22,"is_corresponding":false},{"id":29115,"name":"Sandra L. Lee","orcid":null,"position":23,"is_corresponding":false},{"id":52127,"name":"Mingmei Li","orcid":"0000-0002-5097-2882","position":24,"is_corresponding":false},{"id":52128,"name":"James D. Malley","orcid":"0000-0002-9895-7454","position":25,"is_corresponding":false},{"id":45134,"name":"John H. Malone","orcid":"0000-0003-1369-3769","position":26,"is_corresponding":false},{"id":52129,"name":"Tittu Mathew","orcid":null,"position":27,"is_corresponding":false},{"id":45115,"name":"Nicolas R. Mattiuzzo","orcid":null,"position":28,"is_corresponding":false},{"id":52130,"name":"Mala Munidasa","orcid":null,"position":29,"is_corresponding":false},{"id":1751,"name":"Donna M. Muzny","orcid":"0000-0002-3055-0359","position":30,"is_corresponding":false},{"id":52131,"name":"Fiona Ongeri","orcid":null,"position":31,"is_corresponding":false},{"id":52132,"name":"Lora Perales","orcid":null,"position":32,"is_corresponding":false},{"id":52133,"name":"Teresa M. Przytycka","orcid":"0000-0002-6261-277X","position":33,"is_corresponding":false},{"id":52134,"name":"Ling-Ling Pu","orcid":null,"position":34,"is_corresponding":false},{"id":52135,"name":"Garrett Robinson","orcid":null,"position":35,"is_corresponding":false},{"id":52136,"name":"Rebecca L. Thornton","orcid":null,"position":36,"is_corresponding":false},{"id":52137,"name":"Nehad Saada","orcid":"0000-0001-9903-5913","position":37,"is_corresponding":false},{"id":52138,"name":"Steven E. Scherer","orcid":"0000-0002-3719-3673","position":38,"is_corresponding":false},{"id":52139,"name":"Harold E. Smith","orcid":"0000-0002-3517-5973","position":39,"is_corresponding":false},{"id":52140,"name":"Charles Vinson","orcid":null,"position":40,"is_corresponding":false},{"id":52141,"name":"Crystal B. Warner","orcid":null,"position":41,"is_corresponding":false},{"id":20068,"name":"Kim C. Worley","orcid":"0000-0002-0282-1000","position":42,"is_corresponding":false},{"id":52142,"name":"Yuan-Qing Wu","orcid":null,"position":43,"is_corresponding":false},{"id":52143,"name":"Xiaoyan Zou","orcid":"0000-0003-4574-2350","position":44,"is_corresponding":false},{"id":42996,"name":"David U. Gorkin","orcid":"0000-0003-4944-4107","position":45,"is_corresponding":false},{"id":14693,"name":"Sharon L. R. Kardia","orcid":"0000-0002-9853-3379","position":46,"is_corresponding":false},{"id":35665,"name":"Michael B. Eisen","orcid":"0000-0002-7528-738X","position":47,"is_corresponding":false},{"id":52144,"name":"Fabio Piano","orcid":"0000-0001-9625-7131","position":48,"is_corresponding":false},{"id":52145,"name":"Karin Kionte","orcid":null,"position":49,"is_corresponding":false},{"id":52146,"name":"David H. Fitch","orcid":null,"position":50,"is_corresponding":false},{"id":49667,"name":"Paul W. Sternberg","orcid":"0000-0002-7699-0173","position":51,"is_corresponding":false},{"id":52147,"name":"Asher D. Cutter","orcid":"0000-0001-7141-0013","position":52,"is_corresponding":false},{"id":42965,"name":"Michael O. Duff","orcid":null,"position":53,"is_corresponding":false},{"id":45077,"name":"Roger A. Hoskins","orcid":null,"position":54,"is_corresponding":false},{"id":42997,"name":"Brenton R. Graveley","orcid":"0000-0001-5777-5892","position":55,"is_corresponding":false},{"id":1753,"name":"Richard A. Gibbs","orcid":"0000-0002-1356-5698","position":56,"is_corresponding":false},{"id":17023,"name":"Peter J. Bickel","orcid":"0000-0001-7480-662X","position":57,"is_corresponding":false},{"id":52148,"name":"Artyom Kopp","orcid":"0000-0001-5224-0741","position":58,"is_corresponding":false},{"id":11487,"name":"Piero Carninci","orcid":"0000-0001-7202-7243","position":59,"is_corresponding":false},{"id":45084,"name":"Steven Henikoff","orcid":"0000-0002-7621-8685","position":60,"is_corresponding":false},{"id":45082,"name":"Brian Oliver","orcid":"0000-0002-3455-4891","position":61,"is_corresponding":false},{"id":49666,"name":"Stephen Richards","orcid":"0000-0001-8959-5466","position":62,"is_corresponding":false},{"id":52149,"name":"Zhen‐Xia Chen","orcid":"0000-0003-0474-902X","position":63,"is_corresponding":false},{"id":52150,"name":"Soo Hyung Park","orcid":"0000-0003-4011-3395","position":64,"is_corresponding":false},{"id":52151,"name":"Anthony Fletcher","orcid":"0009-0008-3660-8110","position":65,"is_corresponding":false},{"id":52152,"name":"Peter Fitzgerald","orcid":"0000-0001-8769-0507","position":66,"is_corresponding":false},{"id":44608,"name":"James Brown","orcid":"0000-0001-6027-9179","position":67,"is_corresponding":false},{"id":29113,"name":"Christie Kovar","orcid":null,"position":68,"is_corresponding":false},{"id":52153,"name":"Rebecca Thornton","orcid":"0000-0002-4717-7220","position":69,"is_corresponding":false},{"id":52154,"name":"David Fitch","orcid":"0000-0001-6940-7544","position":70,"is_corresponding":false},{"id":45140,"name":"S Celniker","orcid":"0000-0002-8019-0267","position":71,"is_corresponding":false},{"id":52112,"name":"Zhen-Xia Chen","orcid":null,"position":0,"is_corresponding":true}],"reference_count":65,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"24985915","pmcid":"PMC4079975","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":52.5,"fair_a":55.0,"fair_i":37.5,"fair_r":33.3333,"fair_zscore":-0.4132,"fair_rationale":{"fair_score":44.58,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":52.5,"criteria":[{"key":"f_has_doi","label":"Has a persistent DOI","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"DOI present","rationale":null},{"key":"f_repository_presence","label":"Indexed in repositories / literature DBs","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"datacite=0, pmcid=True, pmid=True","rationale":null},{"key":"f_persistent_ids","label":"Resolvable scholarly identifiers (OpenAlex)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no OpenAlex id","rationale":null},{"key":"f_metadata_richness","label":"Rich, machine-readable metadata","kind":"llm","weight":1.0,"fraction":0.25,"signal":null,"rationale":"The paper does not provide machine-readable metadata; only narrative description of data accessions is given."}]},"A":{"name":"Accessible","score":55.0,"criteria":[{"key":"a_open_access","label":"Open Access / files deposited","kind":"deterministic","weight":1.5,"fraction":1.0,"signal":"Open Access","rationale":null},{"key":"a_retrievable","label":"Free full text retrievable","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"0 OA location(s)","rationale":null},{"key":"a_access_protocol","label":"Clear data/code access protocol","kind":"llm","weight":1.0,"fraction":0.5,"signal":null,"rationale":"Data access protocols are described (e.g., GEO and SRA accession numbers), but no code access or computational workflow is specified."}]},"I":{"name":"Interoperable","score":37.5,"criteria":[{"key":"i_linked_data","label":"Linked datasets / DataCite relations","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"linked_datasets=0, datacite=0","rationale":null},{"key":"i_standard_ids","label":"References data via standard accessions","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"accessions=0, trials=0","rationale":null},{"key":"i_standards","label":"Standard formats, vocabularies & identifiers","kind":"llm","weight":1.0,"fraction":0.75,"signal":null,"rationale":"Standard formats (e.g., FASTQ, BAM) and identifiers (e.g., GenBank accessions, OrthoDB) are used, but vocabulary/ontology usage is not explicitly stated."}]},"R":{"name":"Reusable","score":33.33,"criteria":[{"key":"r_license","label":"Clear, open reuse license","kind":"deterministic","weight":1.5,"fraction":0.0,"signal":"no license","rationale":null},{"key":"r_downloads","label":"Demonstrated reuse (downloads)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"downloads=0","rationale":null},{"key":"r_version","label":"Versioned / maintained","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no version chain","rationale":null},{"key":"r_dataset","label":"Classified as a data resource","kind":"deterministic","weight":0.5,"fraction":1.0,"signal":"is_dataset","rationale":null},{"key":"r_reusability","label":"Data-availability statement, license & reproducibility","kind":"llm","weight":2.0,"fraction":0.5,"signal":null,"rationale":"A data-availability statement and a CC BY-NC 4.0 license are present, but code and detailed metadata to ensure full reproducibility are not provided."}]}},"suggestions":["Provide a structured, machine-readable metadata file (e.g., ISA-Tab or JSON-LD) describing datasets, samples, and protocols.","Share all analysis code in a public repository (e.g., GitHub) with a clear README and software dependencies.","Include persistent identifiers (e.g., DOIs) for each dataset and software version used.","Add detailed sample and experimental metadata using community standards (e.g., MIAME/MINSEQE).","Provide a reproducibility checklist or containerized environment (e.g., Docker) for computational steps."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v2","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v2","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-06-18T00:38:15.674786Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}