GENCODE reference annotation for the human and mouse genomes.

Adam Frankish ,Mark Diekhans ,Magali Ruffier ,Roderic Guigó ,Bianca M Schmitt ,Tomás Di Domenico ,Rory Johnson ,Fiona Cunningham ,Shamika Mohanan ,Paul Muir ,Matthew P Hardy ,Jonathan M Mudge ,Cristina Sisu ,Andrew Berry ,Joel Armstrong ,Sílvia Carbonell Sala ,Daniel R Zerbino ,Sarah Donaldson ,Alexandra Bignell ,Barbara Uszczyńska-Ratajczak ,James C Wright ,Jose M Gonzalez ,Julien Lagarde ,Fábio C P Navarro ,Irina Sycheva ,Jacqueline Chrast ,Andy Yates ,Eloise Stapleton ,Laura Martínez ,Fergal J Martin ,Fernando Campo Del Pozo ,Tim Hubbard ,Carlos García Girón ,M Kellis ,Jyoti S Choudhary ,Jinrui Xu ,Mark Gerstein ,Baikang Pei ,Marie-Marthe Suner ,Benedict Paten ,Bronwen Aken ,Jane Loveland ,Ian T Fiddes ,Toby Hunt ,Osagie Izuogu ,Michael L Tress ,Anne Parker ,Irwin Jungreis ,Alexandre Reymond ,Thibaut Hourlier ,Yan Zhang ,If Barnes ,Tiago Grego ,Anne-Maud Ferreira ,Paul Flicek

doi:10.1093/nar/gky955

Abstract

The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics. Over the last 15 years, the GENCODE consortium has been producing reference quality gene annotations to provide this foundational resource. The GENCODE consortium includes both experimental and computational biology groups who work together to improve and extend the GENCODE gene annotation. Specifically, we generate primary data, create bioinformatics tools and provide analysis to support the work of expert manual gene annotators and automated gene annotation pipelines. In addition, manual and computational annotation workflows use any and all publicly available data and analysis, along with the research literature to identify and characterise gene loci to the highest standard. GENCODE gene annotations are accessible via the Ensembl and UCSC Genome Browsers, the Ensembl FTP site, Ensembl Biomart, Ensembl Perl and REST APIs as well as https://www.gencodegenes.org.

Highlights

Manual and computational annotation workflows use any and all publicly available data and analysis, along with the research literature to identify and characterise gene loci to the highest standard
The GENCODE consortium produces foundational reference genome annotation for the human and mouse genomes as well as tools and data to maintain and improve these annotations
The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics

Summary

Introduction

Manual and computational annotation workflows use any and all publicly available data and analysis, along with the research literature to identify and characterise gene loci to the highest standard. The GENCODE consortium produces foundational reference genome annotation for the human and mouse genomes as well as tools and data to maintain and improve these annotations. Over the last two years, we have focused on two broad areas: completing the first pass manual annotation across the entire mouse reference genome and a dedicated effort to improve the annotation of protein-coding genes in human and mouse.

Results

Conclusion