Overview

The CGAP Gene Finder tool searches the gene database, as defined by UniGene, to find genes as they relate to one specific identifier or based on one or more general criteria. To do this, the tool contains two separate search engines, labeled Specific or General, each with their own entry fields. Either engine can find from one gene to possibly hundreds and the results are returned on a Gene List page. Each gene on this list is then linked to its own Gene Info page that provides gene data and links to various NCBI and NCI databases for that specific gene.

Search Field	Options
Organism	Select "Homo sapiens" or "Mouse" from the drop down box.
Unique Identifier	Choose one of the following: UniGene Cluster ID, e.g., Hs.89552 for human or Mm.37203 for mouse. GenBank Accession Number, e.g., M16594 or AA487452. Gene Symbol, e.g., GSTA2 or DFFA. Notes: (i) Use the wild card symbol (*) to find a family of genes, e.g., GST* will find all the glutathione S-transferase family of genes. (ii) For historical reasons, genes sometimes have more than one gene symbol. However, the Gene Finder can use these alternative gene symbols, e.g., DFF1 will find information about DFFA.

General Search - What Exactly to Put In the Fields

Search Field	Options
Organism	Select "Homo sapiens" or "Mouse" from the drop down box.
Tissue Type	Select a specific tissue from the drop down box or "any".
Function	Select a specific function from the curated cancer gene list in the drop down box or "any".
Cytogenetic Location	Enter a chromosome number to find all the genes on an entire chromosome or a specific locus on a specific chromosome, e.g.: "1" will find all the genes on chromosome 1 "9 44.0" will find all the genes at locus 44.0 on mouse chromosome 9 "6p", "6p12", and 6p12.2 will find the genes in each area for human.
Keyword in Gene Name	Enter any word that is in the gene's descriptive name, e.g., p53, estrogen, hydroxylase, apoptosis, pink.

Examples of "General" Questions You Can Ask

In the General Search, the search criteria are broad and more than one field may be entered at the same time. Thus, the questions you can ask cover a large range, such as:

• What genes have been found to be expressed in human breast tissue? or mouse mammary gland tissue?
• What genes are at the cytogenetic location 6p12.2 in a human? or 9 44.0 in the mouse?
• What genes are involved in human apoptosis?
• Find all the human genes containing the word glutathione in the name?
• In human, what genes are found in breast and are located on chromosome 1?
• In human, what genes are from kidney tissue, and are involved in angiogenesis?
• In mouse, what genes with the word "receptor" in the name are found in brain?
• In mouse, what genes are found in brain, have receptor in the name, and are on chromosome 3?

The results of every Gene Finder query are returned on a Gene List Page. This is a list containing a single gene or several genes that meet the selected search criteria. Associated with each gene is:

• A gene symbol (if it has one)
• A gene name
• A unique sequence ID, which CGAP uses to identify the gene in its database.
• A link to the Gene Info Page

The Gene List page also provides the UniGene Build # that was used to generate the gene list. It is crucial to understand that the Gene Finder search results may vary with each UniGene build (which occurs every few weeks). Please refer to NCBI's UniGene web site to learn more about the UniGene system.

Each gene on the Gene List is linked to its own Gene Info Page where related information about the gene from several NCI and NCBI databases is gathered. Information is presented in two forms:

• Links to databases:
  
  
  • UniGene, an NCBI experimental system generating gene-oriented clusters.
  • LocusLink, an NCBI database providing curated sequence and descriptive information about genetic loci.
  • OMIM, the Online Mendelian Inheritance in Man database which provides a catalog of human genes and genetic disorders.
  • DTP, a search of the NCI's Developmental Therapeutics Program database.
  • cDNA Libraries, to see in which cDNA libraries a particular gene has been found.
  • Cluster Assemblies, a GAI database which has graphically assembled ESTs in the gene clusters.
  • SNPs, a GAI database of single nucleotide polymorphisms in genes.

• Facts, with additional links, about:
  
  
  • Cytogenetic location and Mitelman breakpoint information
  • Sequence-verified clones from IMAGE, which can be purchased
  • Protein similarities
  • Human and mouse orthologs, either curated or computed
  • Presence on curated cancer list(s)