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Abstract

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.

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

“…These included both singleand paired-end reads that are 50 or 75 bases long, sequenced on Illumina platforms (;4 billion reads total; ;175 million reads per sample on average) (Materials and Methods). We integrated those with annotations from RefSeq (Pruitt et al 2002), the UCSC Genome Browser (Hsu et al 2006), and GENCODE (version 4) (Harrow et al 2006) that were processed through our pipeline. We eliminated all annotated non-lincRNA transcripts (e.g., annotated proteincoding genes, microRNAs, tRNAs, and pseudogenes).…”

“…In practice, however, researchers studying human lincRNAs are faced with an excessive set of noncoding transcripts of varying or unknown reliability that may not be well defined (Khalil et al 2009) and have little or no expression data (Harrow et al 2006), or with very small sets of experimentally validated ones (Amaral et al 2010). Transcripts in current annotations of the human transcriptome from the GENCODE/HAVANA (Harrow et al 2006) or the University of California at Santa Cruz (UCSC) Genome Browser (Hsu et al 2006) are valuable resources, but it is hard to evaluate their biological characteristics in the absence of expression levels and further processing.…”

“…Recent genomic studies have shown that a substantial portion of the mammalian genome may be transcribed (Carninci et al 2005), suggesting the presence of many more noncoding transcripts and spurring efforts to catalog them (Carninci et al 2005;Harrow et al 2006) using data collected with tiling microarrays (Bertone et al 2004;Kapranov et al 2007), shotgun sequencing of expressed sequence tags (ESTs) and cloned cDNA (Carninci et al 2005;Birney et al 2007), and maps of histone modification patterns (Guttman et al 2009). In particular, recent studies have focused on large intergenic noncoding RNAs (lincRNAs) (Ponjavic et al 2007;Guttman et al 2009;Khalil et al 2009;Orom et al 2010), which do not overlap annotated protein-coding regions, as this facilitates experimental manipulation and computational analysis.…”

The implications of alternative splicing in the ENCODE protein complement

“…One valuable element of the project has been the detailing of a reference set of manually annotated splice variants by the GENCODE consortium (12). The annotation by the GENCODE consortium is an extension of the manually curated annotation by the Havana team at The Sanger Institute.…”

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

“…Wright et al used OpenMS to to implement a complete proteogenomic analysis workflow, which encompasses database searches using multiple search engines, rescoring and combining of search results, filtering according to various criteria on PSM, peptide and protein levels, and data export -all within OpenMS (Weisser et al in preparation). Processing of over 55 million tandem mass spectra from different publicly available datasets using OpenMS led them to discover over 40 new protein-coding gene annotations in the GENCODE human reference genome [45] . In addition to the identification of novel genes, the information gained in a proteogenomic analysis pertaining to known proteins can also be utilized, for example, to elucidate tissue-specific protein expression levels [46] .…”