Abstract
BackgroundMost human genes produce several transcripts with different exon contents by using alternative promoters, alternative polyadenylation sites and alternative splice sites. Much effort has been devoted to describing known gene transcripts through the development of numerous databases. Nevertheless, owing to the diversity of the transcriptome, there is a need for interactive databases that provide information about the potential function of each splicing variant, as well as its expression pattern.DescriptionAfter setting up a database in which human and mouse splicing variants were compiled, we developed tools (1) to predict the production of protein isoforms from these transcripts, taking account of the presence of open reading frames and mechanisms that could potentially eliminate transcripts and/or inhibit their translation, i.e. nonsense-mediated mRNA decay and microRNAs; (2) to support studies of the regulation of transcript expression at multiple levels, including transcription and splicing, particularly in terms of tissue specificity; and (3) to assist in experimental analysis of the expression of splicing variants. Importantly, analyses of all features from transcript metabolism to functional protein domains were integrated in a highly interactive, user-friendly web interface that allows the functional and regulatory features of gene transcripts to be assessed rapidly and accurately.ConclusionIn addition to identifying the transcripts produced by human and mouse genes, fast DB provides tools for analyzing the putative functions of these transcripts and the regulation of their expression. Therefore, fast DB has achieved an advance in alternative splicing databases by providing resources for the functional interpretation of splicing variants for the human and mouse genomes. Because gene expression studies are increasingly employed in clinical analyses, our web interface has been designed to be as user-friendly as possible and to be readily searchable and intelligible at a glance by the whole biomedical community.
Highlights
Most human genes produce several transcripts with different exon contents by using alternative promoters, alternative polyadenylation sites and alternative splice sites
Fast DB has achieved an advance in alternative splicing databases by providing resources for the functional interpretation of splicing variants for the human and mouse genomes
About 40% of human genes produce at least five different splicing variants (SVs) and up to 10% of them produce more than 10 alternate transcripts each [4,5]
Summary
Much effort has been devoted to setting up the most complete transcript catalogue to date. The scientific community using genomic/transcriptomic databases is increasing in size and diversity, not least because splicing deregulation is involved in many diseases [55], and the use of gene expression studies is continually growing in clinical analyses. We think that fast DB has reached the goal of providing a large number of bioinformatic tools that facilitate the study of the regulation of human gene product expression and of integrating these tools in a user-friendly, attractive and interactive web interface. To display all graphical representations of fast DB (except tissue distribution histograms), the user's web navigator has to contain a flash plugin (freely downloadable at http://www.adobe.com). DA conceived the idea of the database, provided direction for its development and contributed to writing the manuscript
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