Nomenclature: The Language of Genomics

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Nomenclature The Language of Genomics

• Ruth Lovering
• HUGO Gene Nomenclature Committee

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

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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
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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.
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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

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14,363
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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

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Genew Data Flow
Online Genew Search Engine Search
Retrieval Gene Symbol Gene Symbol Gene Name
Gene Name Alias Alias Cytogenetic
Location OMIM Number PMID
Genew Public Data Private Data
Online Text Files http//www.gene.ucl.ac.uk/public
-files/nomen/nomeids.txt http//www.gene.ucl.ac.u
k/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-f
iles/nomen/ens6.txt http//www.gene.ucl.ac.uk/pub
lic-files/nomen/chr20.txt http//www.gene.ucl.ac.u
k/public-files/nomen/chr21.txt http//www.gene.uc
l.ac.uk/public-files/nomen/chr22.txt
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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/ Locus
Link http//www.ncbi.nlm.nih.gov/LocusLink/ MGD,
Mouse Genome Informatics http//www.informatics.ja
x.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/
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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

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Quote of the Day
I would rather use someone elses toothbrush,
than their nomenclature
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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

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Source of Information for Symbol Assignment

• Confidential Submissions
• Literature
• Domain structures
• Other databases
• Specialist advice

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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 Corf (chromosome open reading
frame ) DS (DNA segment number) KIAA
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Chromosome 20
Approved prior to collaboration
Genes without symbols Approved symbols
895
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Chromosome 21
Approved prior to collaboration
Genes without symbols Approved symbols
288
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Chromosome 22
Approved prior to collaboration
Genes without symbols Approved symbols
679
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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

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HUGO Gene Nomenclature Committee
http//www.gene.ucl.ac.uk/nomenclature/ Email
nome_at_galton.ucl.ac.uk
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).