CSIBD connects investigators to the following resources:
GRAIL at the Broad Institute: GRAIL is a tool to examine relationships between genes in different disease associated loci. Given several genomic regions or SNPs associated with a particular phenotype or disease, GRAIL looks for similarities in the published scientific text among the associated genes.
Gene Enrichment Profiler: This database contains expression profiles for ~12,000 genes with NCBI GeneID entry across 126 primary human tissues. Expression profiles were processed to identify tissue specificity which is measured by an enrichment score. High enrichment scores mean higher specificity.The enrichment score is comparable between genes, thus allowing ranking of genes in each tissue profiled. Use the search box to find genes or browse tissues of interest. See Help section for more details.
Web-CREAD: Comprehensive Regulatory Element Analysis and Discovery (CREAD) was developed by Andrew D. Smith and Pavel Summazin while working in Michael Zhang's group in Cold Spring Harbor Labs. CREAD is an open source package that contains many tools that handle the process of matching position weight matrices to genomic sequences. However, these tools require some programming knowledge and a lot of setting up before one can actually start predicting bindings sites.
This web page implements several tools that were employed to identify binding sites in the human genome. The entire genome was processed and analyzed and the results are stored in a database on this server. You may now query any gene or genomic region for the presence of conserved binding sites. Use the menu on the left to start your search.
Current version in the database:
Human genome: HG18 (Mar 2006)
Position weight matrices: Transfac V8.3 and Jaspar V3.0
Web development, implementation and design: Yair Benita & Stephanie Lee (Xavier lab) in close collaboration with Andrew D. Smith.