The GENCODE Project: Encyclopædia of genes and gene variants
Current Gencode version
The current version is Gencode 12, released on the 16/05/2012.
Introduction
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.
Details
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.
The international team working in the GENCODE project is headed by Tim Hubbard at the Wellcome Trust Sanger Institute.
The Gencode gene sets are used by the entire ENCODE consortium and by many other projects (eg. 1000 Genomes) as reference gene sets.
About
The Gencode project is funded through an NHGRI ENCODE grant with additional funding from the Wellcome Trust.
When referencing, please use "Harrow J, et al. (2006) GENCODE: producing a reference annotation for ENCODE" (PubMed).
To assess the current progress of automatic gene building using RNASeq as its primary dataset the RNASeq genome annotation assessment project (RGASP) was launched. For more information about the different phases of this project please use the links on the left.
Working with ENCODE Data
In association with the Biology of Genomes meeting at Cold Spring Harbor Laboratory, we are pleased to announce a one-day workshop on Working with ENCODE Data on Tuesday 8th May, 2012 (9 a.m. to 5 p.m.).
In this workshop, you will learn about the ENCODE Project (ENCyclopedia Of DNA Elements), which has provided a wealth of data sets designed to identify functional elements in the human genome. The workshop will be taught by experts in the field, including Jim Kent and Kate Rosenbloom from UCSC, Bert Overduin from Ensembl and Jen Harrow and Adam Frankish from the GENCODE Consortium. The instructors will guide you through hands-on tutorials for accessing and interpreting ENCODE data in both the UCSC and Ensembl genome browsers. You will need to bring your own wireless-enabled laptop computer to the workshop.
Costs: $100 for the ENCODE workshop only, $250 for the ENCODE workshop plus one night's accommodation. Registration for the Biology of Genomes meeting is a separate process. More information and a detailed agenda can be found on the CSHL website.