Tools
Retired Applications
GoMiner
Addresses the question, "Now that I’ve done the gene expression experiment and identified a set of ‘interesting’ genes, what do those genes mean biologically?" GoMiner batch-processes and organizes lists of thousands or tens of thousands of genes and provides two fluent, robust visualizations of the genes in the framework of the Gene Ontology hierarchy. (Zeeberg, et al., Genome Biology 2003; 4:R28)
HT-GoMiner
High-Throughput GoMiner has the capabilities of GoMiner and a number of others. It automates the analysis of multiple microarrays and integrates results across all of the microarrays, and will be useful in a wide range of applications, including the study of time-courses, evaluation of multiple drug treatments, comparison of multiple gene knock-outs or knock-downs, and screening of large numbers of chemical derivatives generated from a promising lead compound. Zeeberg and Qin, et al., BMC Bioinformatics. 2005 Jul 5;6(1):168.
SpliceMiner
Provides an intuitive non-redundant display of a gene's splice variants and may be searched by gene symbol, chromosomal position, or probe sequence. SpliceMiner is particularly useful in determining which splice variants are targeted (or missed) by a microarray probe, PCR primer, or siRNA. A high-throughput interface is available for batch processing of large numbers of queries. Kahn AB, et al., BMC Bioinformatics. 2007 Mar 5;8(1):75
MatchMiner
Translates among gene identifier types for lists of hundreds or thousands of genes. Included: GenBank accession numbers, IMAGE clone IDs, common gene names, HUGO names, gene symbols, UniGene clusters, FISH-mapped BAC clones, Affymetrix identifiers, and chromosome locations. MatchMiner can also find the intersection of two lists of genes specified by different identifiers. Bussey, et al., Genome Biology 2003; 4:R27
AffyProbeMiner
AffyProbeMiner is to re-define chip definition files (CDFs) for Affymetrix chips taking into account the most recent genomic sequence information. It re-groups probes in Affymetrix chips into probe sets according to a list of non-redundant verified complete coding sequences available in GenBank and RefSeq. Pre-computed CDFs for several chips are available for download. Liu HF, et al., Bioinformatics. 2007 Sep 15;23(18):2385-90.
SpliceCenter
A suite of very user-friendly tools designed for use by every bench biologist who needs to check for the impact of gene splice variation on common molecular biology technologies including RT-PCR, RNAi, expression microarrays, and peptide-based assays. Ryan, et al., BMC Bioinformatics. 2008 9:13
