Explaination for fields in the Search Result:
CGV ID: This is the primary key of each records in CGVdb, and each CGV ID stands for an unique variation. The first five numerical digits use the HGNC ID assigned to individual human genes by HUGO Gene Nomenclature Committee (http://www.gene.ucl.ac.uk/nomenclature/), while the last three digits are just sequential accession number. So it¡¦s possible for the same gene to have multiple records; for example, CGV04057001 stores information about the DNA variation 1387C>T in glucose-6-phosphate dehydrogenase, whereas CGV04057002 stores that of 371A>G in the same gene. A record which has a CGV ID is called a CGV Report.
Gene Name: Gene name approved by HUGO HGNC. For details, see http://www.genenames.org/guidelines.html.
Gene Symbol: Gene symbol approved by HUGO HGNC. For details, see http://www.genenames.org/guidelines.html.
DNA Variation: DNA variation following the notation recommended by HUGO Mutation Database Initiative (MDI). For details, see http://www.interscience.wiley.com/jpages/1059-7794/nomenclature.html.
A.A. Variation: Amino acid variation following the notation recommended by HUGO MDI. For details, see http://www.interscience.wiley.com/jpages/1059-7794/nomenclature.html.
V.R.: The abbreviation of Variation Record that represent a unique variation from one particular reference.
CVR: The abbreviation of Chinese Gene Variation Report. It is the reference that contains phenotype related variations that appear in patient of Chinese origin.
Explanation for fields in respective detailed record (identical fields in the concise display are omitted to avoid redundancy):
NCBI RefSeq: Reference sequence for that gene in NCBI¡¦s Nucleotide database under Entrez.
Reference # (PMID: #): Research papers discussing that gene variation, hyperlinked to NCBI¡¦s PubMed database. Each reference is followed by several more fields recording information derived from that research paper.
Phenotype: Brief OMIM-like description of the phenotype resulted from that gene variation, with hyperlink to OMIN for detailed elucidation.
Relationship with Phenotype: The relationship between variation and phenotype
Ethnic Group: Records the (sub)ethnic group(s) of which the gene variation was described in the original text; if such description exists.
Geographic Location: Geographical information about the occurrence of that gene variation; be provided if deducible from the original PubMed record.
Note from Reference: Conclusive or significant expressions extracted from the original PubMed abstract text.
Value-added external hyperlinks:
Locus Specific DB: Hyperlink to external database specific for that gene; if there is.
HGNC (http://www.genenames.org/):
Approve each known human gene a gene name and symbol (short-form abbreviation). Each symbol is unique and we ensure that each gene is only given one approved gene symbol. It is necessary to provide a unique symbol for each gene so that we and others can talk about them, it also facilitates electronic data retrieval from publications. In preference each symbol maintains parallel construction in different members of a gene family and can also be used in other species, especially the mouse. HGNC has already approved symbols for over 13,000 genes, a third of the estimated total of 30,000 human genes.
Ensembl (http://www.ensembl.org):
Ensembl is a joint project between EMBL-EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on eukaryotic genomes. Ensembl presents up-to-date sequence data and the best possible automatic annotation for eukaryotic genomes. For known genes, structure and location in the genome sequence are predicted. Available now are human, mouse, zebrafish, and mosquito. Others will be added soon.
OMIM (http://www.ncbi.nlm.nih.gov/Omim/):
OMIM is a catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBI. The database contains textual information and references. It also contains copious links to MEDLINE and sequence records in the Entrez system, and links to additional related resources at NCBI and elsewhere. OMIM is intended for use primarily by physicians and other professionals concerned with genetic disorders, by genetics researchers, and by advanced students in science and medicine.
Entrez Nucleotide (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide):
The Entrez Nucleotides database is a collection of sequences from several sources, including GenBank, RefSeq, and PDB. The number of bases grows at an exponential rate.
GeneCards (http://bioinformatics.weizmann.ac.il/cards/):
To test new approaches for the efficient navigation of biomedical information, we have designed the GeneCards Encyclopedia. We use it as a model to develop computational tools that may help to establish an electronic encyclopedia of biological and medical information based on intelligent knowledge navigation technology and a user-friendly presentation of information that makes use of current Human-Computer Interaction research. The GeneCards Encyclopedia integrates a subset of the information stored in major data sources dealing with human genes and their products (with a major focus on medical aspects). Another crucial aspect of the GeneCards strategy is to make use of standard nomenclature, esp. approved gene symbols. Here we link to mirror site in Bioinformatics Lab of National Yang-Ming University (http://genecards.ym.edu.tw).
GeneLynx (http://www.genelynx.org/):
GeneLynx is a service whose aim is to provide the fastest way between an IDENTIFIER for a given HUMAN GENE and all the data available for that gene on the web. It is organized as a set of HYPERLINKS leading to numerous databases and other resources. The number of currently linked resources is 32, and new ones are added regularly.
HGMD (http://www.hgmd.org):
The Human Gene Mutation Database (HGMD) represents an attempt to collate known (published) gene lesions responsible for human inherited disease. This
database, whilst originally established for the study of mutational mechanisms in human genes, has now acquired a much broader utility in that it embodies an up-to-date and comprehensive reference source to the spectrum of inherited human gene lesions. Thus, HGMD provides information of practical diagnostic importance to (i) researchers and diagnosticians in human molecular genetics, (ii) physicians interested in a particular inherited condition in a given patient or family, and (iii) genetic counsellors.
LocusLink (http://www.ncbi.nlm.nih.gov/LocusLink/):
LocusLink provides a single query interface to curated sequence and descriptive information about genetic loci. It presents information on official nomenclature, aliases, sequence accessions, phenotypes, EC numbers, MIM numbers, UniGene clusters, homology, map locations, and related web sites. Sequence accessions include a subset of GenBank accessions for a locus, as well as a new type, the NCBI Reference Sequence (RefSeq).
SwissProt (http://www.expasy.org/sprot/):
SWISS-PROT is an annotated protein sequence database. It was established in 1986 and maintained collaboratively, since 1987, by the group of Amos Bairoch first at the Department of Medical Biochemistry of the University of Geneva and now at the Swiss Institute of Bioinformatics (SIB) and the EMBL Data Library (now the EMBL Outstation - The European Bioinformatics Institute (EBI)). The SWISS-PROT protein knowledgebase consists of sequence entries. Sequence entries are composed of different line types, each with their own format. For standardization purposes the format of SWISS-PROT follows as closely as possible that of the EMBL Nucleotide Sequence Database.
GeneTest-GeneClinics (http://www.genetests.org):
GeneTests-GeneClinics is a medical genetics information resource developed for physicians, other healthcare providers, and researchers, available at no cost to all interested persons. The site includes:
GeneReviews: Expert-authored, peer-reviewed, disease-specific reviews describing the application of genetic testing to the diagnosis, management, and genetic counseling of patients and families with hereditary disorders, and providing links to related resources and databases.
Laboratory Directory: A database of US and international laboratories performing genetic testing, searchable by disease name, gene, OMIM number, lab location, disease feature, services, and director.
Clinic Directory: A database of US and international clinics providing genetic counseling, searchable by geographic location, service provided, and specialty.
Educational Materials: An illustrated glossary of terms used in the GeneReviews, basic information on the use of genetic services, and teaching materials for genetics professionals.
(*Most introduction here are just excerpts, for detailed information please hyperlink to the original sites.)
|
|
