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Nomenclature: The Language of Genomics Ruth Lovering HUGO Gene Nomenclature Committee http://www.gene.ucl.ac.uk/nomenclature/ The Role of HGNC # # # # # Assign approved gene symbols Collate and curate data Maintain symbol database (Genew) Co-ordination with other public databases Guidelines White et al (Genomics 1997) http://www.gene.ucl.ac.uk/nomenclature/guidelines.html Updated guidelines, Genomics April 2002, in press Definition of a Gene HGNC A gene is a DNA segment that contributes to phenotype/function. In the absence of demonstrated function a gene may be characterized by sequence, transcription or homology. [White et al 1997] Definitions Gene name: a brief and specific description which conveys the character or function of the gene/gene product, but does not attempt to describe everything known about it. Gene Symbol: an abbreviation/acronym of the gene name, designated by upper-case Latin letters or by a combination of upper-case letters and Arabic numerals. Approved Symbol # # Unique Meaningful – M55108 – CFTR – cystic fibrosis transmembrane regulator # Systematic – ABCA4 – ATP-binding cassette, sub-family A (ABC1), member 4 # Cross-species – FZD – frizzled Approved Symbols 197 9 198 0 198 1 198 2 198 3 198 4 198 5 198 6 198 7 198 8 198 9 199 0 199 1 199 2 199 3 199 4 199 5 199 6 199 7 199 8 199 9 200 0 200 1 16000 14,363 14000 12000 10000 8000 6000 4000 2000 0 Year Data Management Database: Genew (ver 3.0) # Stable numerate HGNC IDs # Sequence data store, local BLAST # Automatic updates from Locuslink, GDB, MGD, SWISS-PROT # Streamlined tracking system for correspondence # Will be upgraded to enable online editing Genew Data Flow Other Database Files Online Genew Search Engine LocusLink: Approved Symbol, LocusLink ID, OMIM ID, RefSeq SWISS-PROT: Approved Symbol, SWISSPROT ID, Sequence Accession ID GDB: Approved Symbol, GDB ID, Gene Name, Cytogenetic Location MGD: Reserved mouse gene symbols and names. (Not Exported) Search Gene Symbol Gene Name Alias Retrieval Gene Symbol Gene Name Alias Cytogenetic Location OMIM Number PMID Genew Public Data Private Data Data Submissions Authors Journals Literature Review Chromosome Sequencing Projects Gene Families Homologs from other species Online Text Files http://www.gene.ucl.ac.uk/public-files/nomen/nomeids.txt http://www.gene.ucl.ac.uk/public-files/nomen/ens1.txt http://www.gene.ucl.ac.uk/public-files/nomen/ens2.txt http://www.gene.ucl.ac.uk/public-files/nomen/ens3.txt http://www.gene.ucl.ac.uk/public-files/nomen/ens4.txt http://www.gene.ucl.ac.uk/public-files/nomen/ens5.txt http://www.gene.ucl.ac.uk/public-files/nomen/ens6.txt http://www.gene.ucl.ac.uk/public-files/nomen/chr20.txt http://www.gene.ucl.ac.uk/public-files/nomen/chr21.txt http://www.gene.ucl.ac.uk/public-files/nomen/chr22.txt Databases Using Approved Symbols Ensembl http://ensembl.ebi.ac.uk/ GENATLAS http://bisance.citi2.fr/GENATLAS/ GeneCards http://bioinformatics.weizmann.ac.il/cards/ The Genome Database (GDB) http://gdbwww.gdb.org/ Human Gene Mutation Database http://www.hgmd.org/ LocusLink http://www.ncbi.nlm.nih.gov/LocusLink/ MGD, Mouse Genome Informatics http://www.informatics.jax.org/ Online Mendelian Inheritance in Man http://www.ncbi.nlm.nih.gov/Omim/ SWISS-PROT http://www.expasy.ch/sprot/ UCSC Human Genome Project Working Draft http://genome.cse.ucsc.edu/ The Benefits of Approved Nomenclature # # # # # # One gene symbol User friendly Simplified information retrieval Database co-ordination Efficient use of resources Systematic assignment of new symbols Quote of the Day: “I would rather use someone else’s toothbrush, than their nomenclature” When Do You Name a Gene? # # # When you want to publish it When you want to talk about it When you want to add it to a database But only when you have some information about it Source of Information for Symbol Assignment # # # # # Confidential Submissions Literature Domain structures Other databases Specialist advice Symbol Assignment by Sequence Identical sequence # Verify approved symbol Highly similar # Assign next available symbol in the family series Highly similar, known pseudogene # Assign a symbol in the family series with the suffix “P” Moderately similar # Assign appropriate symbol with the suffix “L” for like No Homology # C#orf# (chromosome # open reading frame #) # D#S# (DNA segment number) # KIAA# Chromosome 20 Approved prior to collaboration 242 Currently approved 288 653 Genes without symbols Approved symbols 607 895 Chromosome 21 Approved prior to collaboration 118 Currently approved 36 170 Genes without symbols Approved symbols 252 288 Chromosome 22 Approved prior to collaboration 70 Currently approved 281 609 398 Genes without symbols Approved symbols 679 Why Use Approved Nomenclature? # # # # # # # Standardisation Communication of information Manual curation Data storage, management and analysis Community collaboration Consistency across species Linking genes to disease and physiology HUGO Gene Nomenclature Committee http://www.gene.ucl.ac.uk/nomenclature/ Email: [email protected] Dr Sue Povey Dr Hester Wain Dr Elspeth Bruford Dr Ruth Lovering Dr Michael Lush Dr Mathew Wright The work of the HGNC is supported by NIH contract N01-LM-9-3533 (60% total) and by the UK Medical Research Council (40%).