Database of peptides detected from a re-analysis of the experiments in the PeptideAtlas and GPM databases. These peptides are mapped to the protein sequences annotated for the 20,481 genes in GENCODE (release 12). We have included all peptides that can be mapped at a corrected false discovery rate of 2%.
The National Human Genome Research Institute (NHGRI) launched a public research consortium named ENCODE, the Encyclopedia Of DNA Elements, in September 2003, to carry out a project to identify all functional elements in the human genome sequence. After a successful pilot phase on 1% of the genome, the scale-up to the entire genome is now underway. The Wellcome Trust Sanger Institute was awarded a grant to carry out a scale-up of the GENCODE project for integrated annotation of gene features.
The aim of GENCODE as a sub-project of the ENCODE scale-up project is to annotate all evidence-based gene features in the entire human genome at a high accuracy. The result will be a set of annotations including all protein-coding loci with alternatively transcribed variants, non-coding loci with transcript evidence, and pseudogenes. The process to create this annotation involves manual curation, different computational analysis and targeted experimental approaches. Putative loci can be verified by wet-lab experiments and computational predictions will be analysed manually.
