Hedgehog Signaling Pathway Database

Oh, those crazy geneticists! Who thinks of naming a gene “Hedgehog”, anyway? The name may be frivolous, but the Hedgehog Signaling Pathway is certainly not, as it is required during the embryogenesis of many organisms. The Hedgehog Signaling Pathway Database, through the San Francisco State University, provides a number of online tools for researchers studying this pathway. There are diagrams of Hedgehog signal transduction (though not the most polished diagrams I’ve ever seen), a list of genes involved in Hedgehog signaling, and a list of Hedgehog-related diseases and human mutations (along with links to relevant clinical trials). Additionally, the “Stem Cells” tab provides links to scientific papers related to stem cells and the Hedgehog pathway. Sadly, the “Hedgehog Expression in Tissues” page is still under construction, so I would continue to check back as this site continues to develop.

hedgehog.sfsu.edu

Sight Seer

Regulating gene expression by transcription factors is fundamental to the survival of every cell. The web is bursting with tools for identifying these proteins and their DNA-binding sites, but few offer a visual perspective. Since seeing is believing, and insightful for understanding too, Paul Boardman at Manchester University developed SightSeer, a tool for imaging mapped transcription factor binding sites upstream of eukaryotic genes. Users paste FASTA-formatted sequence data into a box then select an organism from an impressively long list. SightSeer uses TRANSFAC and SCPD databases for mapping binding locations on the DNAs. Options for narrowing searches are available as well.

[www.chick.manchester.ac.uk/SiteSeer]

Structure Conjuncture

“What if they gave a war and nobody came?” In the new millennium, that rather irreverent 1960s question has been turned on its head to “what if we had a database and no one annotated it?” Welcome to PDBWiki, the web site that aims to enhance the quality of data in the Protein Database (PDB) through community-supplied knowledge. With over 61,000 entries, PDB has a lot of room for commenting and this is what PDBWiki aims to provide. Several options are available, including comments/questions, relevant links, and discussions. PDBWiki's legion of knowledgeable followers will, no doubt, help to increase the accuracy of PDB entries, at no cost, to boot. Kudos to all involved for their ongoing efforts on this important resource.

http://pdbwiki.org/index.php/Main_Page

Edinburgh Mouse Atlas Project

This is an excellent site that will make researchers who study mice jump for joy (and just might make researchers who choose other model organisms a bit envious). The Edinburgh Mouse Atlas Project offers many tools for researchers, divided into the 3-D embryo anatomy atlas and the EMAGE gene-expression database. The embryo anatomy atlas does offer three dimensions (as promised), as one can move through transverse, frontal, or sagittal slices of embryos at different developmental stages, as well as watch animations of a complete embryo. The EMAGE database provides in situ hybridization gene-expression data in the embryo across developmental time. One can search by gene name, anatomy, or embryo space (a neat tool in which you color an area of the embryo and search for any genes that have expression within that region). Additionally (if I haven’t yet convinced you to visit the site), you can request CDs of the mouse atlas data, free of charge for academic use.
www.genex.hgu.mrc.ac.uk

Fluish Dynamics

As pandemics go, H1N1 fits into the category of a fairly manageable one (there is a vaccine, after all). Yet, the public perception of the illness is disturbingly inaccurate, thanks to its scary portrayal in the media. Paddling upstream against the current of misinformation about this important public health matter is the Influenza Research Database, which deals with research data and serves scientists in the field with timely information and computing utilities. The primary focus is on search/analysis tools, including a considerable amount of sequence information and protein structure data, a workbench for collecting online data (login required), and numerous standard sequence analysis tools. Links to influenza news sources round out the offerings.

[www.fludb.org]