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Human & Mouse Orthologous Gene Nomenclature (HUMOT)

Human & Mouse Orthologous Gene Nomenclature (HUMOT). HUGO Gene Nomenclature Committee (HGNC) Matt Wright. http://www.gene.ucl.ac.uk/nomenclature/. The Role of HGNC. Assign unique approved gene names and symbols Co-ordinate with other databases and nomenclature groups

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Human & Mouse Orthologous Gene Nomenclature (HUMOT)

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  1. Human & Mouse Orthologous Gene Nomenclature (HUMOT) HUGO Gene Nomenclature Committee (HGNC) Matt Wright http://www.gene.ucl.ac.uk/nomenclature/

  2. The Role of HGNC • Assign unique approved gene names and symbols • Co-ordinate with other databases and nomenclature groups • Collate and curate data (Genew)

  3. Searchgenes http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl

  4. Gene Symbol Report

  5. Why Use Approved Nomenclature? • Standardisation • User friendly • Communication • Manually curated • Consistency across species

  6. Stable Unique Memorable Meaningful Naming Criteria

  7. Symbol Assignment • Sequence comparison • Information from literature • Information from researchers • Domain structures • Information from other databases

  8. HUMOT • Two dedicated HUMOT editors • Approve the same gene symbol for each human/mouse ortholog pair • Human gene symbols are written in all uppercase letters (e.g. human PON3) • Mouse only the first letter is uppercase and the rest are lowercase (e.g. mouse Pon3).

  9. Definitions Mouse Gene • Orthologs Related by speciation (and preferably by function) • Paralogs Related by gene duplication Rat Gene Common Ancestral Gene Human Gene 1 Human Gene 2

  10. Determining Orthology • Best BLAST hit, Reciprocal BLAST Searched with approved symbol PON3 http://www.ensembl.org

  11. BLAST Problems • Unequal rates of evolution • Hidden paralogy • Large numbers of genomes Human Gene 1 Mouse Gene 1 Rat Gene 1 Mouse Gene 1 Mouse Gene 2 Human Gene 2 Rat Gene 2 Human Gene Mouse Gene 2 Hidden paralogy Unequal rates

  12. Determining Orthology • Best BLAST hit, Reciprocal BLAST • Conserved Synteny

  13. Conserved Synteny HUMAN MOUSE (taken from doegenomes.org)

  14. Human Location 7q21.3 7q21.3 7q21.3 Mouse Symbol Pon1 Pon2 Pon3 Mouse Location 6 A2 6 A1 6 A1 Human Symbol PON1 PON2 PON3 Conserved Synteny Searched with approved symbol PON2 http://www.ncbi.nlm.nih.gov/mapview

  15. Determining Orthology • Best BLAST hit, Reciprocal BLAST • Conserved Synteny • Phylogeny

  16. PON1 PON2 PON3 Phylogeny http://phigs.jgi-psf.org/ Searched with approved symbol PON1

  17. Orthology Resources Provider HGNC: MGI: NCBI: Ensembl: JGI: ANGIS: Resource HUMOT Consensus Orthology Search Mammalian Orthology Query Oxford Grid Comparative Maps Human/Mouse Orthology Map Homologene MapViewer ‘Orthologue Predictions’ in Ensembl gene reports PhIGs Search PhIGs Synteny Viewer Oxford Grid

  18. Consensus Orthology Search • HGNC, MGI, Homologene, Ensembl and PhIGs orthology assertions • Will include approved symbols and names, DNA sequences, database identifiers, aliases, and chromosomal locations for each putative ortholog pair. http://www.gene.ucl.ac.uk/humot/cos

  19. Determining Orthology • Best BLAST hit, Reciprocal BLAST • Conserved Synteny • Phylogeny • Orthology Resources • WE DO NOT MAKE AN ORTHOLOGOUS ASSERTION IF RESULTS ARE UNCLEAR

  20. HGNC HUMOT Activities • 2,500 curated orthology assertions • 7,000 consensus orthology assertions • Examine human/mouse orthologs with different approved symbols • Eradicating mis-mapped data

  21. MGI Oxford Grid A section from the MGI Oxford Grid (September 2004) mouse chromosomes human 270 mouse chromosome 6 genes with orthologs on human chromosome 7

  22. Oxford Grid Singletons A section from the MGI Oxford Grid (April 2005) mouse chromosomes human 279 mouse chromosome 6 genes with orthologs on human chromosome 7

  23. Future Work • Continue to assign orthologous gene nomenclature • Provide common nomenclature for human/mouse orthologs with different symbols • Utilise the large cDNA data sets such as those from the H-Invitational and RIKEN to rapidly identify and assign parallel nomenclature

  24. cDNA Data Sets • Gene structures • Secondary/Tertiary Structure • Possible functions • Encoded functional domains • Sub-cellular localizations

  25. Prof Sue Povey (Chair) Dr Elspeth Bruford (Project Co-ordinator) Dr Michael Lush Dr Ruth Lovering (HUGOA Editor) Dr Matt Wright (HUMOT Editor) Dr Varsha Khodiyar Dr Tam Sneddon Fabrice Ducluzeau Conover Talbot Jr. Dr Tina Eyre HGNC Team (Senior Bioinformatician) Dr Kate Sneddon The work of the HGNC is supported by the Wellcome Trust, NHGRI grant P41 HG003345 and the UK Medical Research Council.

  26. http://www.gene.ucl.ac.uk/nomenclature/

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