Websites - Disease-related Databases

Cancer Chromosomes contains three databases: the NCI/NCBI SKY/M-FISH & CGH Database, the NCI Mitelman Database of Chromosome Aberrations in Cancer, and the NCI Recurrent Aberrations in Cancer.  As such, this integrated system is searchable for cancer or tissue type, cytogenetic location or for diagnostic criteria.  All information has interactive links with the 29 other NCBI databases.

OBRC: Online Bioinformatics Resources Collection at http://www.hsls.pitt.edu/guides/genetics/obrc

Biologists who lament, "So many databases, so little time," should check out this portal from the University of Pittsburgh in Pennsylvania. The site provides brief descriptions of more than 1500 free bioinformatics databases and tools in categories such as immunology, genomics, and RNA. If you're looking for data on how pathogens alter gene activity in immune cells, for instance, follow the link to the Macrophage Expression Atlas in the U.K. Or the site can help you sift through the more than 70 databases with information on plant genes and proteins.

SIEGE: Smoking Induced Epithelial Gene Expression Database.

Shah, V et al., 2005. Nucleic Acids Res. 33:D573-D579

Abstract

The SIEGE (Smoking Induced Epithelial Gene Expression) database is a clinical resource for compiling and analyzing gene expression data from epithelial cells of the human intra-thoracic airway. This database supports a translational research study whose goal is to profile the changes in airway gene expression that are induced by cigarette smoke. RNA is isolated from airway epithelium obtained at bronchoscopy from current-, former- and never-smoker subjects, and hybridized to Affymetrix HG-U133A Genechips, which measure the level of expression of approximately 22,500 human transcripts. The microarray data generated along with relevant patient information is uploaded to SIEGE by study administrators using the database's web interface, found at http://pulm.bumc.bu.edu/siegeDB. PERL-coded scripts integrated with SIEGE perform various quality control functions including the processing, filtering and formatting of stored data. The R statistical package is used to import database expression values and execute a number of statistical analyses including t-tests, correlation coefficients and hierarchical clustering. Values from all statistical analyses can be queried through CGI-based tools and web forms found on the 'Search' section of the database website. Query results are embedded with graphical capabilities as well as with links to other databases containing valuable gene resources, including Entrez Gene, GO, Biocarta, GeneCards, dbSNP and the NCBI Map Viewer.

Journal Link | PMID

Comments