GENCODE: producing a reference annotation for ENCODE

By J. Harrow, F. Denoeud, Adam Frankish, Alexandre Reymond, Chao-Kung Chen, Jacqueline Chrast, Julien Lagarde, J. Gilbert, R. Storey, D. Swarbreck and 5 more. Genome Biology, 2006

695 citations recorded by the source corpus.

BackgroundThe GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manual annotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results.ResultsThe GENCODE gene features are divided into eight different categories of which only the first two (known and novel coding sequence) are confidently predicted to be protein-coding genes. 5' rapid amplification of cDNA ends (RACE) and RT-PCR were used to experimentally verify the initial annotation. Of the 420 coding loci tested, 229 RACE products have been sequenced. They supported 5' extensions of 30 loci and new splice variants in 50 loci. In addition, 46 loci without evidence for a coding sequence were validated, consisting of 31 novel and 15 putative transcripts. We assessed the comprehensiveness of the GENCODE annotation by attempting to validate all the predicted exon boundaries outside the GENCODE annotation. Out of 1,215 tested in a subset of the ENCODE regions, 14 novel exon pairs were validated, only two of them in intergenic regions.ConclusionIn total, 487 loci, of which 434 are coding, have been annotated as part of the GENCODE reference set available from the UCSC browser. Comparison of GENCODE annotation with RefSeq and ENSEMBL show only 40% of GENCODE exons are contained within the two sets, which is a reflection of the high number of alternative splice forms with unique exons annotated. Over 50% of coding loci have been experimentally verified by 5' RACE for EGASP and the GENCODE collaboration is continuing to refine its annotation of 1% human genome with the aid of experimental validation.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/63209f51ce48cc7ab7b1a2362beaa63848a341b5

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Citations in the corpus

ENCODE whole-genome data in the UCSC Genome Browser: update 2012 (2011, background): “The Gencode Gene set (12) has been updated to version 7 (May 2011).”
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes (2007, background): “The recent EGASP experiment (Harrow et al ., 2006) shows that (1) computational methods are still less accurate than experts, and (2) even where experimental data is plentiful, some novel genes can still be predicted and verified.”
The UCSC Genome Browser database: extensions and updates 2011 (2011, background): “Gencode Genes version 7 (24) was released, as were three releases of the Ensembl Genes (6,25) data set.”
A User's Guide to the Encyclopedia of DNA Elements (ENCODE) (2011, methodology): “html, and references therein), and the Sanger Center [20] are combined to produce a consensus pseudogene set.”
HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease (2015, methodology): “Location of variants relative to genes was calculated us-ing BEDTools and both GENCODE (15) and RefSeq (16).”
Fast Computation and Applications of Genome Mappability (2012, methodology): “Influence of mismatch values and read lengths on the mappability of the human projected transcriptome as defined by GENCODE [ 8 ] .”
annotatr: Genomic regions in context (2016, methodology): “We use GENCODE long non-coding RNAs (lncRNA) from GENCODE at the transcript level (Harrow, 2006).”
OpenMS: a flexible open-source software platform for mass spectrometry data analysis (2016, methodology): “Processing of more than 55 million tandem mass spectra from different publicly available data sets using OpenMS led them to discover more than 40 new protein-coding gene annotations in the GENCODE human reference genome 44 .”
Integrative annotation of chromatin elements from ENCODE data (2012, neutral): “Supplementary Data are available at NAR Online: Supplementary Tables 1–7, Supplementary Figures 1–23, Supplementary Methods, Supplementary Results and Supplementary References [44–62].”
The GENCODE pseudogene resource (2012, background): “The annotation of all pseudogenes in the human reference genome is part of the wider effort by the GENCODE consortium that also aims to identify all proteincoding, long non-coding RNA (lncRNA) and short RNA genes [28,29].”
firestar—advances in the prediction of functionally important residues (2011, methodology): “We ran ﬁrestar for all 798 genes in chromosomes 21 and 22 annotated by Gencode in their 3C release (18).”
AlleleSeq: analysis of allele-specific expression and binding in a network framework (2011, methodology): “…for RNA-Seq where we also build maternal and paternal versions of the gene annotation (including, most importantly, splice-junction library) by mapping the GENCODE annotation (GENCODE 3c annotation is available from the UCSC Genome Browser; Harrow et al , 2006) onto the personal diploid genome.”
Ensembl 2011 (2010, methodology): “The consensus mouse gene set continues to be a merge of Ensembl and Havana annotation, incorporating improvements developed as part of the GENCODE merge process.”