ArticleG3 (Bethesda, Md.)2015
Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data.
Article in G3 (Bethesda, Md.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 84 citations in OpenAlex.
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- Comparative gene annotation and orthology assignments across 301 species of Drosophilidae.bioRxiv : the preprint server for biology · 2026Article
- Comparative gene annotation and orthology assignments across 301 species of Drosophilidae.PLoS biology · 2026Article
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- Meiotic Sex Chromosome Inactivation: Conservation across the Drosophila genus.PLoS genetics · 2025Article
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- Diversely evolved xibalbin variants from remipede venom inhibit potassium channels and activate PKA-II and Erk1/2 signaling.BMC biology · 2024Article
- Identification of antennal alternative splicing by combining genome and full-length transcriptome analysis inFrontiers in physiology · 2024Article
- Machine learning-aided scoring of synthesis difficulties for designer chromosomes.Science China. Life sciences · 2023Article
- Influence of RVFV Infection on Olfactory Perception and Behavior inPathogens (Basel, Switzerland) · 2023Article
- Distinct developmental mechanisms influence sexual dimorphisms in the milkweed bugProceedings. Biological sciences · 2023Article
- A Computational Workflow for Analysis of 3' Tag-Seq Data.Current protocols · 2023Article
- Proteomic analysis of Sarcoptes scabiei reveals that proteins differentially expressed between eggs and female adult stages are involved predominantly in genetic information processing, metabolism and/or host-parasite interactions.PLoS neglected tropical diseases · 2022Article
- Identification and Tissue Expression Profiles of Odorant Receptor Genes in the Green Peach AphidInsects · 2022Article
- Manual annotation ofF1000Research · 2022Article
- A transcription factor DAF-5 functions in Haemonchus contortus development.Parasites & vectors · 2021Article
- Article
Corrections and comments
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Authors and funding
13 authors at 2 institutions in 1 country.
Funding
Abstract
We report the current status of the FlyBase annotated gene set for Drosophila melanogaster and highlight improvements based on high-throughput data. The FlyBase annotated gene set consists entirely of manually annotated gene models, with the exception of some classes of small non-coding RNAs. All gene models have been reviewed using evidence from high-throughput datasets, primarily from the modENCODE project. These datasets include RNA-Seq coverage data, RNA-Seq junction data, transcription start site profiles, and translation stop-codon read-through predictions. New annotation guidelines were developed to take into account the use of the high-throughput data. We describe how this flood of new data was incorporated into thousands of new and revised annotations. FlyBase has adopted a philosophy of excluding low-confidence and low-frequency data from gene model annotations; we also do not attempt to represent all possible permutations for complex and modularly organized genes. This has allowed us to produce a high-confidence, manageable gene annotation dataset that is available at FlyBase (http://flybase.org). Interesting aspects of new annotations include new genes (coding, non-coding, and antisense), many genes with alternative transcripts with very long 3' UTRs (up to 15-18 kb), and a stunning mismatch in the number of male-specific genes (approximately 13% of all annotated gene models) vs. female-specific genes (less than 1%). The number of identified pseudogenes and mutations in the sequenced strain also increased significantly. We discuss remaining challenges, for instance, identification of functional small polypeptides and detection of alternative translation starts.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.