Database for Glycan Structures

Sasisekharan, Ram

Abstract

There is accumulating evidence for the role of glycans in cell growth and development, tumor growth and metastasis, anticoagulation, immune response and microbial pathogenesis. In support of the importance of the study of glycans as a fundamental field, through the 'glue grant initiative', the NIGMS funded the Consortium for Functional Glycomics [CFG; www.functionalglycomics.org] in 2001. The CFG is organized into 7 scientific Cores that provide state-of-the-art facilities for glycan analysis, glycan synthesis, screening glycan-GBP interactions, exclusive gene microarrays for investigating the expression of genes related to glycomics, generation and phenotyping transgenic mice containing knock outs of different genes pertaining to GBPs or glycoenzymes. ? ? An integral component of the CFG is the Bioinformatics Core [housed at MIT] whose primary objective is to acquire, integrate and disseminate, in a meaningful fashion, the diverse data sets generated by the CFG. The Bioinformatics Core of the CFG has made significant progress in developing the necessary infrastructure and software applications, to acquire diverse datasets generated by the CFG, annotate and organize them in object based relational databases and disseminate them in a meaningful fashion. The relational databases have been central to integration and dissemination of CFG data via molecule pages for GBPs and glycoenzymes. The molecule page provides an integrated presentation of information from public databases such as SwissProt, GenBank, PDB, LocusLink, GEO, OMIM, etc. along with the new data generated by the CFG for a given GBP or glycoenzyme molecule. In addition to GBP and glycoenzyme molecule pages, a part of CFG's focus is to develop a database that would support and facilitate the assignment of glycan structures in the glycoprofiling of tissues. Development of Glycan databases similar to the GBP and glycoenzyme molecule pages will be very valuable and useful to the glycobiology community and beyond. However, at the present time, since the available resources for glycans are fragmented and stymied with numerous issues, their integration is beyond the scope and resources of the 'glue grant' that funds CFG. ? ? Based on the above, it can be summarized that there is a practical need to rapidly develop a glycan database that not only integrates the data derived from the different scientific cores of CFG, but also from other defined resources. This forms the framework for the present STTR grant application as a fast-track Phases I and II grant application that is highly integrated towards addressing the requirements of the glycomics field. ? ?