-omics

-omics

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Cross-sectional analysis of the various hierarchical levels in which the expression of biological information is organized in the cell.

 

Introductory reading

The Encode project is a current paradigm for the integration of multiple -omics datasets for comprehensive annotation of the human genome.

ENCODE Project Consortium (2011) A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 9:e1001046. (pmid: 21526222)

[ PubMed ] [ DOI ] Abstract The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.

 

Contents

See also: -omics.

• Genome, Epigenome, Variome
• Transcriptome, Exome
• Proteome, Regulome, Secretome, Kinome (cf. Kinases)
• Glycome
• Lipidome
• Metabolome, Reactome
• Phenome, Physiome

See also: List of omics topics in biology

   

Further reading and resources

ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57-74. (pmid: 22955616)

[ PubMed ] [ DOI ] Abstract The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.

Samuels & Rouleau (2011) The case for locus-specific databases. Nat Rev Genet 12:378-9. (pmid: 21540879)

[ PubMed ] [ DOI ] Abstract Locus-specific databases are the most useful repositories of the sequence information underlying medical genetic conditions and, for this reason, they need our continued support.