GENCODE: producing a reference annotation for ENCODE
| Autor: | Harrow, J., Denoeud, F., Frankish, A., Reymond, A., Chen, C. K., Chrast, J., Julien Lagarde, Gilbert, J. G., Storey, R., Swarbreck, D., Rossier, C., Ucla, C., Hubbard, T., Antonarakis, S. E., Guigo, R. |
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| Přispěvatelé: | Universitat Pompeu Fabra |
| Předmět: |
Bioinformàtica
Humans Gene Loci ddc:576.5 RNA Messenger ENCODE Expressed Sequence Tags Proteins/ genetics GENCODE RACE Genome Human Sequence Analysis RNA Research RNA Messenger/analysis Computational Biology Proteins Chromosome Mapping Genomics Sequence Analysis DNA Reference Standards Computational Biology/methods/ standards Genes Computational Biology/methods Computational Biology/standards Genomics/methods Genomics/standards Proteins/genetics Pseudogenes Genomics/methods/ standards Biologia molecular -- Tècnica cDNA |
| Zdroj: | Recercat. Dipósit de la Recerca de Catalunya instname Genome Biology, Vol. 7, No Suppl 1 (2006) pp. S4.1-9 Genome Biology Scopus-Elsevier Genome Biology, vol. 7 Suppl 1, pp. S4.1-S4.9 |
| ISSN: | 1465-6906 |
| Popis: | Background: The 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/nannotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results./nResults: The GENCODE gene features are divided into eight different categories of which only/nthe first two (known and novel coding sequence) are confidently predicted to be protein-coding/ngenes. 5’ rapid amplification of cDNA ends (RACE) and RT-PCR were used to experimentally/nverify the initial annotation. Of the 420 coding loci tested, 229 RACE products have been/nsequenced. They supported 5’ extensions of 30 loci and new splice variants in 50 loci. In addition,/n46 loci without evidence for a coding sequence were validated, consisting of 31 novel and 15/nputative transcripts. We assessed the comprehensiveness of the GENCODE annotation by/nattempting to validate all the predicted exon boundaries outside the GENCODE annotation. Out/nof 1,215 tested in a subset of the ENCODE regions, 14 novel exon pairs were validated, only two/nof them in intergenic regions./nConclusions: In total, 487 loci, of which 434 are coding, have been annotated as part of the/nGENCODE reference set available from the UCSC browser. Comparison of GENCODE/nannotation with RefSeq and ENSEMBL show only 40% of GENCODE exons are contained within/nthe two sets, which is a reflection of the high number of alternative splice forms with unique/nexons annotated. Over 50% of coding loci have been experimentally verified by 5’ RACE for/nEGASP and the GENCODE collaboration is continuing to refine its annotation of 1% human/ngenome with the aid of experimental validation. |
| Databáze: | OpenAIRE |
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