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Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

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GENCODE: the reference human genome annotation for The ENCODE Project.

Jennifer Harrow¹, Adam Frankish, Jose M Gonzalez

¹Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambridge CB10 1SA, United Kingdom. jla1@sanger.ac.uk

Genome Research

|September 8, 2012

Summary

This summary is machine-generated.

The GENCODE Consortium

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Area of Science:

Genomics
Transcriptomics
Bioinformatics

Background:

The GENCODE Consortium provides comprehensive human genome annotation.
Previous releases focused on protein-coding genes, with increasing attention to alternative splicing.

Purpose of the Study:

To detail the GENCODE 7 release, emphasizing its expanded annotation of long noncoding RNAs (lncRNAs) and coding transcripts.
To assess the completeness of the GENCODE 7 annotation using experimental and computational evidence.

Main Methods:

Computational analysis of human genome data.
Manual annotation and experimental validation.
Integration of RNA-sequencing (RNA-seq) data (Illumina Body Map 2.0).

Main Results:

GENCODE 7 includes 20,687 protein-coding and 9640 long noncoding RNA loci.
Identified 33,977 coding transcripts not present in UCSC genes and RefSeq.
RNA-seq data revealed 3689 new potential loci, many likely unannotated lncRNAs.
Assessed annotation completeness: 35% of transcription start sites supported by CAGE, 62% of protein-coding genes have polyA sites, and over one-third supported by mass spectrometry data.

Conclusions:

GENCODE 7 offers the most extensive publicly available annotation of long noncoding RNA loci.
The annotation continues to expand, particularly in alternative splicing and noncoding RNAs.
Ongoing integration of new data sources like RNA-seq is crucial for improving genome annotation completeness.