NAR Molecular Biology Database Collection entry number 742

http://pulm.bumc.bu.edu/siegeDB

Shah, V.¹, Sridhar, S. 1, Beane, J. 1, Brody, J. 2 and Spira, A. 1,2

¹Bioinformatics Program, College of Engineering, Boston University, 44 Cummington Street, Boston, MA 02215
² Pulmonary Center and Department of Medicine, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118

Contact vshah@bu.edu

The SIEGE 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 directly 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 serve to perform various quality control functions including the processing, filtering and formatting of the stored data. The R statistical package is used to directly import database expression values and execute a number of statistical tests including T-Tests, correlation coefficients and hierarchical clustering. Results from all statistical analyses can be queried and retrieved through CGI-based tools and web forms found on the “Search” section of database website. Furthermore, results from statistical queries are embedded with visualization and graphing utilities along with hot links to other databases containing valuable gene resources including Entrez Gene, GO, Biocarta, GeneCards, dbSNP and NCBI Map Viewer.

We are grateful to Michael Schaffer for his expert advice on the use of appropriate database software and server configuration. This work was supported in part by a Doris Duke Charitable Foundation Clinical Scientist Development Award (A.S.) and by the National Institutes for Health Grant HL47049. Affymetrix provided the U133A arrays for these studies.

Go to the abstract in the NAR 2005 Database Issue.

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