%0 Journal Article
%T SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies
%A Michael C Ryan
%A Barry R Zeeberg
%A Natasha J Caplen
%A James A Cleland
%A Ari B Kahn
%A Hongfang Liu
%A John N Weinstein
%J BMC Bioinformatics
%D 2008
%I BioMed Central
%R 10.1186/1471-2105-9-313
%X A number of contemporary technologies are used for analyzing transcripts or proteins. To enable investigation of the impact of splice variation on the interpretation of data derived from those technologies, we have developed SpliceCenter. SpliceCenter is a suite of user-friendly, web-based applications that includes programs for analysis of RT-PCR primer/probe sets, effectors of RNAi, microarrays, and protein-targeting technologies. Both interactive and high-throughput implementations of the tools are provided. The interactive versions of SpliceCenter tools provide visualizations of a gene's alternative transcripts and probe target positions, enabling the user to identify which splice variants are or are not targeted. The high-throughput batch versions accept user query files and provide results in tabular form. When, for example, we used SpliceCenter's batch siRNA-Check to process the Cancer Genome Anatomy Project's large-scale shRNA library, we found that only 59% of the 50,766 shRNAs in the library target all known splice variants of the target gene, 32% target some but not all, and 9% do not target any currently annotated transcript.SpliceCenter http://discover.nci.nih.gov/splicecenter webcite provides unique, user-friendly applications for assessing the impact of transcript variation on the design and interpretation of RT-PCR, RNAi, gene expression microarrays, antibody-based detection, and mass spectrometry proteomics. The tools are intended for use by bench biologists as well as bioinformaticists.Technologies commonly used by biologists to investigate gene function include quantitative RT-PCR (qRT-PCR) assays, RNA interference (RNAi) mediated by small interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs), gene expression microarrays, and antibody-based protein assays. Each of those technologies targets a small nucleic or amino acid sequence that, preferably, is unique to a specific gene.More than 60% of protein-coding genes in vertebrates exhibit splice va
%U http://www.biomedcentral.com/1471-2105/9/313