GENCODE
GENCODE provides high-quality reference gene annotations for human and mouse genomes, integrating experimental evidence (CAGE clusters, polyA sites, mass spectrometry peptide evidence) and computational analysis to classify protein-coding genes, long noncoding RNAs (lncRNAs), alternative splicing transcripts, transcription start sites, and promoter characteristics.
Key Features:
- Integration of Experimental and Computational Approaches: Combines manual annotation and computational analysis with publicly available datasets and research literature to characterize gene loci.
- Comprehensive Annotation Database: Annotates protein-coding genes, long noncoding RNA (lncRNA) loci, and alternative splicing transcripts, with GENCODE release 7 containing over 20,687 protein-coding and 9,640 lncRNA loci.
- Experimental Validation: Supports annotations with CAGE clusters for transcription start sites, polyA sites for transcript ends, and peptide evidence from mass spectrometry for protein-coding genes.
- Innovative Bioinformatics Tools and Infrastructure: Develops bioinformatics tools and infrastructure to create and refine transcript structures and determine function, enabling targeted annotation efforts such as SARS-CoV-2-related annotations.
- Focus on lncRNAs: Provides comprehensive characterization of lncRNAs including their generation pathways, histone-modification profiles, splicing signals, and selective pressures in promoter regions.
Scientific Applications:
- Basic Genomic Research: Serves as a reference annotation resource for human and mouse genome biology.
- Clinical Genomics: Supports clinical genomics and variant interpretation by providing reference gene structures.
- Transcriptomics and Splicing Studies: Enables analysis of alternative splicing, transcript diversity, and transcription start site usage.
- lncRNA Research: Facilitates investigation of lncRNA biology, promoter characteristics, and selective pressures.
- Proteomics Validation: Provides peptide-level support from mass spectrometry for validation of protein-coding gene annotations.
- Targeted Annotation Efforts: Supports targeted annotation projects related to specific biological questions, including SARS-CoV-2.
Methodology:
Manual annotation combined with computational analysis integrates publicly available datasets and research literature with experimental evidence (CAGE clusters, polyA sites, mass spectrometry peptides) using developed bioinformatics tools and infrastructure.
Topics
Details
- License:
- Other
- Maturity:
- Mature
- Cost:
- Free of charge
- Tool Type:
- web application
- Operating Systems:
- Linux, Windows, Mac
- Programming Languages:
- Java, Perl, Python, Ruby
- Added:
- 6/27/2019
- Last Updated:
- 11/24/2024
Operations
Publications
Frankish A, Diekhans M, Ferreira A, Johnson R, Jungreis I, Loveland J, Mudge JM, Sisu C, Wright J, Armstrong J, Barnes I, Berry A, Bignell A, Carbonell Sala S, Chrast J, Cunningham F, Di Domenico T, Donaldson S, Fiddes IT, García Girón C, Gonzalez JM, Grego T, Hardy M, Hourlier T, Hunt T, Izuogu OG, Lagarde J, Martin FJ, Martínez L, Mohanan S, Muir P, Navarro FCP, Parker A, Pei B, Pozo F, Ruffier M, Schmitt BM, Stapleton E, Suner M, Sycheva I, Uszczynska-Ratajczak B, Xu J, Yates A, Zerbino D, Zhang Y, Aken B, Choudhary JS, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Paten B, Reymond A, Tress ML, Flicek P. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Research. 2018;47(D1):D766-D773. doi:10.1093/nar/gky955. PMID:30357393. PMCID:PMC6323946.
Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, Rodriguez JM, Ezkurdia I, van Baren J, Brent M, Haussler D, Kellis M, Valencia A, Reymond A, Gerstein M, Guigó R, Hubbard TJ. GENCODE: The reference human genome annotation for The ENCODE Project. Genome Research. 2012;22(9):1760-1774. doi:10.1101/gr.135350.111. PMID:22955987. PMCID:PMC3431492.
Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I, Berry A, Bignell A, Boix C, Carbonell Sala S, Cunningham F, Di Domenico T, Donaldson S, Fiddes IT, García Girón C, Gonzalez JM, Grego T, Hardy M, Hourlier T, Howe KL, Hunt T, Izuogu OG, Johnson R, Martin FJ, Martínez L, Mohanan S, Muir P, Navarro FCP, Parker A, Pei B, Pozo F, Riera FC, Ruffier M, Schmitt BM, Stapleton E, Suner M, Sycheva I, Uszczynska-Ratajczak B, Wolf MY, Xu J, Yang YT, Yates A, Zerbino D, Zhang Y, Choudhary JS, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Paten B, Tress ML, Flicek P. GENCODE 2021. Nucleic Acids Research. 2020;49(D1):D916-D923. doi:10.1093/nar/gkaa1087. PMID:33270111. PMCID:PMC7778937.
Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigó R. The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Research. 2012;22(9):1775-1789. doi:10.1101/gr.132159.111. PMID:22955988. PMCID:PMC3431493.
Documentation
Downloads
- Biological datahttps://www.gencodegenes.org/human/releases.html#Human GENCODE Gene Set - Release history
- Biological datahttps://www.gencodegenes.org/mouse/releases.htmlMouse GENCODE Gene Set - Release history