GENCODE: the reference human genome annotation for the ENCODE, project

Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
Genome Research (Impact Factor: 14.63). 09/2012; 22(9):1760-74. DOI: 10.1101/gr.135350.111


The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites. Over one-third of GENCODE protein-coding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. New models derived from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently in GENCODE, of which 3127 consist of two exon models indicating that they are possibly unannotated long noncoding loci. GENCODE 7 is publicly available from and via the Ensembl and UCSC Genome Browsers

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    • "The potential PCR clones in each library were removed using Stacks:clone_filter program (Cole et al, 2005) to keep unique reads. The reads in each library were further screened for mapping to reference genome (hg19, GRCh37 including all alternative haplotypes), transcriptome (GENECODEv19 comprehensive transcripts (Harrow et al, 2012); RefSeq genes; human all mRNAs (Pruitt et al, 2005); USCS genes (Hsu et al, 2006); Ensemble genes (Hubbard et al, 2002); lincRNAs (Trapnell et al, 2010); and human ribosomal RNA sequences); abundant sequences (vector sequences [http://]; phage sequences (Leinonen et al, 2011); and polyA/C sequences), bacterial rRNA sequences (Cole et al, 2005), and bacterial and viral genomic sequences (Leinonen et al, 2011). "
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    • "All obtained reads from each sample were mapped against the human genome (hg19 build) with Bowtie/Tophat v2.0.2, which allows mapping across splice sites by reads segmentation (Trapnell et al., 2012). The uniquely mapped reads were subsequently assembled into transcripts guided by reference annotation (Gencode v14 and RefSeq gene models) (Harrow et al., 2012; Pruitt et al., 2012)wit hCu fflinks v2.0.2 (Trapnell et al., 2012). The expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments). "
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