GENCODE


The GENCODE Project: Encyclopædia of genes and gene variants


Background

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.

Having been involved in successfully delivering the definitive annotation of functional elements in the human genome, the GENCODE group were awarded a second grant in 2013 in order to continue their human genome annotation work and expand GENCODE to include annotation of the mouse genome.

The GENCODE gene sets are used by the entire ENCODE consortium and by many other projects (eg. 1000 Genomes) as reference gene sets.


Current GENCODE Goals

The aims of the current GENCODE phase running from 2013 to 2017, as a sub-project of the ENCODE scale-up project are:

The mouse annotation data will allow comparative studies between human and mouse and likely improve annotation quality in both genomes. 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 human GENCODE resource will continue to be available to the research community with quarterly releases of Ensembl genome browser (mouse data will be made available with every other release), while the UCSC genome browser will continue to present the current release of the GENCODE gene set.

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.


Participants photograph, Gencode workshop 2014

Participants photograph, Gencode workshop 2014

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Participants, PI & Co-PIs

List of all participants


GENCODE collaborators

We are working in close collaboration with various other research groups around the world. These include the NCBI (eg. Kim Pruitt, CCDS project), CSHL (Tom Gingeras group) and others.

Please contact us if you would like to start a collaboration with the GENCODE project.


Acknowledgements

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. (2012) GENCODE: The reference human genome annotation for The ENCODE Project" (PubMed) or "Mudge JM and Harrow J (2015) Creating reference gene annotation for the mouse C57BL6/J genome assembly" (PubMed).

 
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