Note changed place: Lister Hill Auditorium, today, Tuesday, 11 AM.

"Cancer Chromosomes" a new Entrez database, 
Karl Sirotkin, IEB, NCBI

Three databases, the NCI Mitelman Database of Chromosome Aberrations in
Cancer, 
the NCI Recurrent Aberrations in Cancer database, and the NCI/NCBI
SKY/M-FISH & CGH Database, will soon be incorporated into NCBI's Entrez
system as "CancerChromosomes."  This database makes it possible to search
for cytogenetic, clinical, and reference information from the Mitelman
database, which contains over 44,000 clinical cases, and the SKY/M-FISH &
CGH online interactive database (<http://www.ncbi.nlm.nih.gov/sky/skyweb.cgi>)
for human and mouse clinical and research data. The latter database includes
the display of SKY/M-FISH data in colored ideograms, with each chromosome
displayed in its unique classification color with band overlay (a SKYGRAM),
and CGH profiles. Queries are performed using the same approach as other
Entrez databases such as PubMed, and searches are performed using any of
three methods: Entrez query box, simple search, and advanced search. The
main features of this integrated database are (1) seamless searching of
karyotypic, SKY/M-FISH, and CGH data, based on the underlying cytogenetic
features of the aberrations they demonstrate; (2) the ability to find
similar cases based on textual content, which means that all information,
including cytogenetics terms such as chromosome bands, is converted into
pseudo-words in a pseudo-document; and (3) the ability to display common
elements in a list of cases or clones/cells, based either on textual content
or common cytogenetic changes.  Searches based on case information, such as
diagnosis and site, result in a case-based report (i.e., a list of all cases
displaying the searched element), while searches based on underlying
cytogenetic features are displayed as a clone/cell report. Several unique
manipulations can be performed on the reports resulting from a  search.  For
each case from the SKY/M-FISH & CGH database, there are links to the
SKYGRAM, CGH profile, clinical and other information (e.g., FISH data), and
the abstract in PubMed; cases from the Mitelman database are linked to the
karyotypic, clinical, and reference information in the Mitelman database.
There are also links from each case to other cases with related cytogenetic
and/or clinical characteristics.   Detailed reports, which can be generated
for each case, list all chromosomal breakpoints, chromosomal junctions,
numerical and structural abnormalities, and bands gained and lost, and can
be displayed at different levels of band resolution.   A unique feature of
this database is the similarity report, which shows the similarities of
diagnosis, tumor site, and cytogenetic abnormalities, including those seen
in CGH profiles, among any number of selected cases. This new Entrez
database makes it possible to search for commonalities among cases, data
critical to the search for new genes, such as oncogenes and tumor
suppressors, which lie at the root of cancer.  The talk will focus on
potential use of the psuedo documents for global analyses in collaboration.