MatchMiner: a tool for batch navigation among gene and gene product identifiers

Abstract

MatchMiner is a freely available program package for batch navigation among gene and gene product identifier types commonly encountered in microarray studies and other forms of 'omic' research. The user inputs a list of gene identifiers and then uses the Merge function to find the overlap with a second list of identifiers of either the same or a different type or uses the LookUp function to find corresponding identifiers.

Figure 1

Information Flow in MatchMiner. Input identifier lists are first translated into unique internal gene indices to form a translation table. The translation table is then either converted into another set of identifiers using the LookUp function or compared with another such table using the Merge function to generate a report showing the intersection of two separate identifier lists. The resulting output can be displayed as HTML or else saved as text for import into other programs.

Figure 2

Database relational table schema for MatchMiner. (a) Logical database representation. Data are incorporated from the UCSC Human Genome Build, LocusLink, UniGene, OMIM, and the Affymetrix annotation sets for HU95 and HU133 chips. Each candidate gene is assigned a gene index in the GeneIdx table. These gene indexes are used as keys for all of the MatchMiner operations. The number of many-to-many relationships in the model illustrates the complexity of the data. (b) Physical representation of the database. The implementation currently includes 14 tables with about 12 million rows.

Figure 3

Associating FISH-mapped BACs with genes. Schematic view of FISH-mapped BACs from 1p36.33 near the PITSLRE kinase genes (UCSC Genome Browser, June 2002 freeze). Note that a single BAC can encompass one or more genes. In MatchMiner, the FISH-mapped BAC table from UCSC is imported, and chromosomal positions are read from the table for comparison with the transcriptional start positions of UCSC 'Known Genes'. If a transcriptional start is contained within the bounds of a BAC, that BAC is associated with the corresponding gene index. Thus, a BAC containing several genes will be associated with each of those genes.