The transcription factor encyclopedia.

Here we present the Transcription Factor Encyclopedia (TFe), a new web-based compendium of mini review articles on transcription factors (TFs) that is founded on the principles of open access and collaboration. Our consortium of over 100 researchers has collectively contributed over 130 mini review articles on pertinent human, mouse and rat TFs. Notable features of the TFe website include a high-quality PDF generator and web API for programmatic data retrieval. TFe aims to rapidly educate scientists about the TFs they encounter through the delivery of succinct summaries written and vetted by experts in the field. TFe is available at http://www.cisreg.ca/tfe.

A regulatory toolbox of MiniPromoters to drive selective expression in the brain.

The Pleiades Promoter Project integrates genomewide bioinformatics with large-scale knockin mouse production and histological examination of expression patterns to develop MiniPromoters and related tools designed to study and treat the brain by directed gene expression. Genes with brain expression patterns of interest are subjected to bioinformatic analysis to delineate candidate regulatory regions, which are then incorporated into a panel of compact human MiniPromoters to drive expression to brain regions and cell types of interest. Using single-copy, homologous-recombination "knockins" in embryonic stem cells, each MiniPromoter reporter is integrated immediately 5' of the Hprt locus in the mouse genome. MiniPromoter expression profiles are characterized in differentiation assays of the transgenic cells or in mouse brains following transgenic mouse production. Histological examination of adult brains, eyes, and spinal cords for reporter gene activity is coupled to costaining with cell-type-specific markers to define expression. The publicly available Pleiades MiniPromoter Project is a key resource to facilitate research on brain development and therapies.

The Gene Set Builder: collation, curation, and distribution of sets of genes.

BACKGROUND: In bioinformatics and genomics, there are many applications designed to investigate the common properties for a set of genes. Often, these multi-gene analysis tools attempt to reveal sequential, functional, and expressional ties. However, while tremendous effort has been invested in developing tools that can analyze a set of genes, minimal effort has been invested in developing tools that can help researchers compile, store, and annotate gene sets in the first place. As a result, the process of making or accessing a set often involves tedious and time consuming steps such as finding identifiers for each individual gene. These steps are often repeated extensively to shift from one identifier type to another; or to recreate a published set. In this paper, we present a simple online tool which - with the help of the gene catalogs Ensembl and GeneLynx - can help researchers build and annotate sets of genes quickly and easily. DESCRIPTION: The Gene Set Builder is a database-driven, web-based tool designed to help researchers compile, store, export, and share sets of genes. This application supports the 17 eukaryotic genomes found in version 32 of the Ensembl database, which includes species from yeast to human. User-created information such as sets and customized annotations are stored to facilitate easy access. Gene sets stored in the system can be "exported" in a variety of output formats - as lists of identifiers, in tables, or as sequences. In addition, gene sets can be "shared" with specific users to facilitate collaborations or fully released to provide access to published results. The application also features a Perl API (Application Programming Interface) for direct connectivity to custom analysis tools. A downloadable Quick Reference guide and an online tutorial are available to help new users learn its functionalities. CONCLUSION: The Gene Set Builder is an Ensembl-facilitated online tool designed to help researchers compile and manage sets of genes in a user-friendly environment. The application can be accessed via http://www.cisreg.ca/gsb/.

Tendon reattachment to a metallic implant using an allogenic bone plate augmented with rhOP-1 vs. autogenous cancellous bone and marrow in a canine model.

Functionality of endoprosthetic reconstruction may be improved through secure and lasting soft tissue reattachment directly to the metallic implant surface. Tendon reattachment to the metallic surface of a titanium implant (enhanced tendon anchor, ETA) using autogenous bone plate as an interpositional structure between the tendon and metal, augmented with autogenous bone chips and marrow, provided successful mechanical and functional outcome. However, preparation of the autogenous bone plate is not practical in a clinical setting, but application of an allogenic bone plate could be an alternative. The autogenous cancellous bone and marrow may also be substituted by bone growth factors so that no autogenous bone graft is required. We hypothesized that the reconstitution of the direct tendon-bone insertion morphology in tendon reattachment to metallic implant could be achieved using allogenic cancellous bone plate augmented with autogenous cancellous bone and marrow, and that the autogenous bone grafts could be replaced by recombinant human osteogenic protein-1 (rhOP-1). In two canine groups the supraspinatus tendon was reattached unilaterally to a modified ETA implant with a highly porous metallic surface known as Tritanium Dimensionalized Metal. Allogenic bone plates saturated with rhOP-1-collagen putty were used in the OP-1 (OP) group, while plates saturated with autogenous cancellous bone and marrow were used in the bone marrow (BM) group. Functional, radiographical, mechanical and histomorphological analysis results were compared between both groups. At 15 weeks, gait analysis showed 78% and 81% recovery of preoperative weight-bearing in OP and BM groups, respectively. The calcified area around the tendon in OP group was 5.2 times larger than that in BM group (p<0.001). The ultimate tensile strength of the reattachment was 24% and 38% of the intact contralateral side in OP and BM groups, respectively, without significant difference between them. There was evidence of tendon-bone insertion transitional zones, tissue ingrowth and adhesion to the metallic surface in both groups. In conclusion, the use of the allograft combined with rhOP-1 had a similar effect as combined with autogenous cancellous bone and marrow in the tendon reattachment to the metallic surface.