HSLS Update

Searching Entrez Gene

Entrez Gene, developed by the National Center for Biotechnology Information (NCBI), is an excellent Databases for finding gene specific information. This resource is useful for providing answers, when you need to:

• Gather information for a particular gene, including its genomic sequence, mRNA sequences for all known isoforms, intron/exon arrangements, chromosomal localization, genetic variations and expression.
• View a complete list of genes present, for example, on human chromosome 3.
• Know which genes on chromosome 3 are associated with a known disease.

Each Entrez Gene record represents a single gene from a given organism, and provides information including nomenclature, chromosomal localization, gene products, markers, phenotypes, molecular interaction, genomic sequence information, intron/exon organization, links to literature citations, sequences, homologs, protein domains, variation details, maps and expression.

As of September 2004, more than 2400 taxa are represented in the database, which contains a total of 958,000 records. Approximately 95% of all records represent protein-coding genes.

The following step-by-step examples are some of the ways to obtain gene specific information from Entrez Gene. A hands-on workshop, Genetic Information Hubs, includes additional techniques for searching Entrez Gene. Check the HSLS class calendar <www.hsls.pitt.edu/services/instruction/calendar> for future class offerings, or you may schedule a group or individual consultation with Ansuman Chattopadhyay, PhD, HSLS information specialist in molecular biology and genetics resources (ansuman@pitt.edu or 412-648-1297). Visit the HSLS molecular biology and genetics Web portal at <www.hsls.pitt.edu/guides/genetics/>
for more HSLS tools, resources, and tutorials.

How to use Entrez Gene: Step-by-step Examples

Query 1: Find gene specific information for human BRCA1

Go to Entrez Gene
<www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene>

1) Type BRCA1 [Gene name] in the search box.

2) Click on 'Limits'.

3) Select 'RefSeqs' from the 'Include Only' field. (For more information about searching RefSeq, see HSLS Update, October 2004, pages 5-6 <www.hsls.pitt.edu/about/news/hslsupdate/2004/october/search_refseq/>.

4) Select 'Homo sapiens' from the 'Limit by Taxonomy' field.

5) Click 'Go'.

The default summary display page will appear. It provides gene specific links to many resources (Map Viewer, Nucleotide, OMIM etc) via the 'Links' menu on the top right of the page.

6) Click on hyperlinked gene name to get the full report page.

7) On the Gene Report page, click on the accession number of the genomic contig that contains the gene (NC_000017) to get the entire genomic sequence for this gene.

Also on the Gene Report page, the accession numbers assigned to the mRNAs (e.g.NM_007297) and proteins (e.g. NP_009228) are shown at the left and right, for each isoform of human BRCA1.

8) On the left of the screen, the mRNA accession number for each isoform of BRCA1 appears (as blue links). Click on any accession number to retrieve the corresponding nucleotide sequence.

9) On the right of the screen, the protein links are listed (as red links) for each isoform. Click on any protein link to retrieve the protein sequence.

10) Click on 'Links' to get the links menu of several NCBI and non-NCBI resources that have information specifically for this gene. For example, selecting 'SNP' and 'Gene View in dbSNP' will provide all single nucleotide polymorphism data known for this gene, while clicking on 'GEO profiles' will give you information regarding its gene expression.

More Entrez Gene Examples

Query 2: View a complete list of genes present on human chromosome 3

1) Go to Entrez Gene.

2) Type 3[chr] in the search box.

3) Click 'Go'.

Query 3: Retrieve a list of genes from chromosome 3, which are also associated with schizophrenia

1) Go to Entrez Gene.

2) Type 3[chr] AND schizophrenia [dis] in the search box.

3) Click 'Go'.

--Ansuman Chattopadhyay