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LocusLink module of the MLA course on Introduction to Molecular Biology Information Resources
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Searching Example: human colon cancer

Open Entrez Gene:
  • search for human colon cancer to find genes that might be involved in some way with that disease
    • no need to use quotes or use field specifiers, etc. for the purpose of this sample search. Just view the Details to see how Entrez parsed and handled the search. As you know by now, the search for "human" was not restricted to the [Organism] field since we did not use a field specifier, so we can expect hits from other organisms as well.

  • the "docsum" (document summary) page provides only brief information about each gene record retrieved by your search, and is analagous to the list of authors/article titles you first see in a PubMed search result -- you need to view the records in a format other than "summary" in order to see their complete content.

  • Some records are marked with red text that notes they were discontinued or replaced with other GeneIDs.

    • As is true for most molecular biology databases, the records are a work in progress and are subject to change as scientists learn more about the genes. For example, some gene records are generated as a result of gene prediction during analysis of an organism's genome. If the sequence data and/or gene prediction algorithm change over time -- that is, if new data are added in a subsequent genome build or refinements are made to the gene prediction software -- some records might be discontinued. Other records, particularly those for known genes, persist from one genome build to another, but the information in the record will continue to be updated as new knowledge is acquired.
    • To exclude records that have since been discontinued or replaced, use the Limits page and select the option for Include Only: Current Records. Then press the Go button beside the query box at the top of the page to apply the Limit to your search.

  • Other tips about the Limits page:

    • Note that the Limits page for Entrez Gene, as for other Entrez databases, gives you a good idea on how users might want (or find it helpful) to search. For example, it allows users to restrict their search to specific types of records, such as known genes, or specific RefSeq status codes.
    • Some options shown on the page, such as Limit by Taxonomy, provide only a subset of the choices that are actually available. The organisms and higher taxa shown on that page tend to be of common interest, though a user can search by any other organism or taxonomic level using the [Organism] field in Entrez Gene, or by using the NCBI Taxonomy Browser and then linking to the Gene records that exist for that organism or taxon. Note, however, that not all organisms or taxa in the NCBI Taxonomy Browser will have records in Entrez Gene, because Gene has a more limited scope than the Entrez Nucleotide and Protein databases.

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Revised 11/06/2007