Can GoMiner analyze splice variants?
GoMiner and High-Throughput GoMiner (referred to in the following collectively as ‘GoMiner’) traditionally dereplicate total and changed gene input files so that only one instance of a gene name is processed. When multiple alternatively spliced forms are to be analyzed, however, dereplication would result in a loss of relevant information. Consequently, we have added a new feature to GoMiner to retain full information about the alternative splice variants by replicating the input of each gene by the number of alternative exons per gene in total and changed gene input files. As a specific example, suppose that a microarray platform contained probes that were unique for two different splice variants of BRCA1. Then the two splice variants would be designated in the input files as ‘BRCA1~1’ and ‘BRCA1~2’. The ‘~’ tells GoMiner to treat these as different entries, rather than to de-replicate them, but to ignore the suffix when querying the GO database. By this mechanism, all splice variants
