GENCODE reference annotation for the human and mouse genomes

By Adam Frankish, Mark Diekhans, Anne-Maud Ferreira, Rory Johnson, Irwin Jungreis, J. Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, J. Armstrong and 45 more. Nucleic Acids Res., 2018

2,759 citations recorded by the source corpus.

Abstract The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics. Over the last 15 years, the GENCODE consortium has been producing reference quality gene annotations to provide this foundational resource. The GENCODE consortium includes both experimental and computational biology groups who work together to improve and extend the GENCODE gene annotation. Specifically, we generate primary data, create bioinformatics tools and provide analysis to support the work of expert manual gene annotators and automated gene annotation pipelines. In addition, manual and computational annotation workflows use any and all publicly available data and analysis, along with the research literature to identify and characterise gene loci to the highest standard. GENCODE gene annotations are accessible via the Ensembl and UCSC Genome Browsers, the Ensembl FTP site, Ensembl Biomart, Ensembl Perl and REST APIs as well as https://www.gencodegenes.org.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/62cd63ca22adc48692873429164c6251258753dd

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Citations in the corpus

Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches (2022, positive): “For every targeted gene all full-length protein-coding transcript sequences from the ENSEMBL database were used as design targets if the isoform had the GENCODE annotation tag ‘basic’ (Frankish et al., 2019; Yates et al., 2020).”
Ensembl 2020 (2019, neutral): “Each Ensembl/GENCODE transcript tagged as part of MANE Select has a corresponding RefSeq accession with an identical splicing pattern and identical untranslated regions.”
The UCSC Genome Browser database: 2021 update (2020, methodology): “Striving to keep data up-to-date, new updates to gene annotations include GENCODE Genes, NCBI RefSeq Genes, and Ensembl Genes.”
Tximeta: Reference sequence checksums for provenance identification in RNA-seq (2019, methodology): “These reference transcripts may be 3 downloaded from a database such as GENCODE, Ensembl, or RefSeq [1–3] in the form 4 of nucleotide sequences in FASTA format and/or transcript locations in a genome in 5”
GENCODE: reference annotation for the human and mouse genomes in 2023 (2022, background): “GENCODE builds reference quality human and mouse annotation of protein-coding genes, long non-coding RNAs (lncRNAs) and small non-coding RNAs (sRNAs), as well as pseudogenes of protein-coding genes and immunoglobulin and T-cell receptor segments (1,2).”
Structural variant calling: the long and the short of it (2019, background): “Indeed, annotations are typically incomplete, even for well-characterized organisms such as humans [90], let alone for non-model organisms.”
WHSC1 monomethylates histone H1 and induces stem-cell like features in squamous cell carcinoma of the head and neck (2020, methodology): “In brief, after quality assessment, paired-end sequence reads were aligned to human reference transcriptome with GENCODE gene annotation (v29, GRCh38 primary assembly) [25] by Kallisto in the strand-specific mode (v0.”
Ensembl 2021 (2020, neutral): “We have enriched our reference human transcript annotation, which is created as part of the GENCODE consortium (18).”