In this issue

Transitioning from LocusLink to Entrez Gene

Cancer Chromosomes: a New Entrez Database

HomoloGene: An Entrez Database with a New Look

BLAST Link (BLink) to Protein Alignments and Structures

Debut of the HCT Database and Anthropology/Allele Frequencies in dbMHC

350kb Sequence Length Limit Removed by Sequence Database Collaboration

New Eukaryotic Genomes at NCBI

Environmental Samples Make Big Splash

HIV Protein-Interaction Database

e-PCR and Reverse e-PCR: Greater Sensitivity, More Options

New Organisms in UniGene

RefSeq Accession Numbers Get Longer as Rat Gets Last 6-digit Accession

Slots available for FieldGuidePlus Training Course Onsite at NCBI

RefSeq Release 6 on FTP Site

Exponential Growth of GenBank Continues with Release 142

Entrez Tools is a 'Hot Spot'

BLAST Lab: Using BLASTClust

New Microbial Genomes in GenBank

Entrez Quiz


Cancer Chromosomes: a New Entrez Database

Three databases, the NCI/NCBI SKY (Spectral Karyotyping)/M-FISH (Multiplex-FISH) and CGH (Comparative Genomic Hybridization) Database, the NCI Mitelman Database of Chromosome Aberrations in Cancer, and the NCI Recurrent Chromosome Aberrations in Cancer databases are now integrated into NCBI’s Entrez system as the “Cancer Chromosomes” database. Cancer Chromosomes supports searches for cytogenetic, clinical, or reference information using the flexible Entrez search and retrieval system. Search tips are provided in the Help document at:

Search “Cancer Chromosomes” from the database pulldown menu on the NCBI home page or navigate to the “Cancer Chromosomes” page for advanced searches via the link on the Entrez home page at:

Three search formats are offered on the Entrez Chromosomes home page: a conventional Entrez Query, a Quick/Simple Search, and an Advanced Search. The Entrez Query is performed using the search box at the top of the page, and, as with other Entrez databases, searches may be combined using term limits and Boolean expressions. The Simple Search, available via a link in the sidebar on the Cancer Chromosomes page, offers a set of menus from which one may select search terms to indicate a disease site or diagnosis. These terms can be combined with specifications for a particular chromosomal location and anomaly. The Advanced Search form, also linked from the sidebar, is arranged similarly. This form contains three main sections, labeled Cytogenetic, Clinical, and Reference, which offer a combination of forms and menus of search terms to help in the construction of complex queries. Diagnostic terms vary among databases; the SKY/M-FISH database uses ICD-3-O terms, whereas the Mitelman and Recurrent databases use a different system. The menus include all ICD-O-3 terms entered into the database to date and all terms used in the Mitelman and Recurrent databases. Descriptions of the sections and terms indexed are given in the Help document.

Searches based on case information, such as diagnosis and disease site, return a “case-based report” that lists all cases matching the query terms. Searches based on underlying cytogenetic features are displayed as a “clone/cell report” in which each clone or cell-line is listed separately. The number of cases or cells/clones found for each search is displayed at the top of the results page, broken down into three totals: the total matches found in the SKY/M-FISH & CGH Database, the total matches found in the Mitelman database, and the total matches from the Mitelman Recurrent Database.

From the results list, users can access the pull-down menu and display a variety of features, including the corresponding literature from PubMed, the results as a list of UI (unique identifier) numbers, or view related reports based on common cytogenetic or diagnostic features. Users can also view Similarity reports, which show terms common to a group or records within several term categories such as diagnosis/site and cytogenetic abnormalities (including CGH) among the selected cases or clones/cells. Term co-occurences are listed at several levels: common to all cases, common to 50%-90% of cases, and common to less than 50% of cases. The common term or abnormality is shown in the left column and the number of affected cases is shown in the right column. The cytogenetic abnormalities are shown at all levels of resolution. Select ‘Similarity Report (High Resolution Only)’ to see similarities at a high level of resolution such as chromosome band.

The results of a sample query for records dealing with breakpoints of the chromo-somal band 8q is shown in Figure 1.

Click on image to view larger

Figure 1: Results of an Entrez Cancer Chromosomes search for records using the query "8q". The number of cases from each database is given at the top of the result summary. Clicking on the 'Details' link shows how the query was interpreted by Entrez.

Links in the search results summary lead to full reports such as the Case report #1437 shown in Figure 2.

Click on image to view larger

Figure 2 : Detailed display of Case report #1437, with written karyotype, case summary, graphic display of colored ideogram, and chromosome abnormalities in tabular format.

Display buttons provide access to additional views of the data such as chromosomal diagrams or a table view. Users can also access the case details or link to related resources from the original search summary by way of the Entrez Links menu.


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NCBI News | Fall/Winter 2002 NCBI News: Spring 2003