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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
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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
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Unique
Meaningful
– M55108
– CFTR
– cystic fibrosis transmembrane regulator
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Systematic
– ABCA4
– ATP-binding cassette, sub-family A (ABC1), member 4
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Cross-species
– FZD
– frizzled
Approved
Symbols
197
9
198
0
198
1
198
2
198
3
198
4
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16000
14,363
14000
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10000
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2000
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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
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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?
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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
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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?
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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%).