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

Bussey KJ, Kane D, Sunshine M, Narasimhan S, Nishizuka S, Reinhold WC, Zeeberg B, Ajay W, Weinstein JN - Genome Biol. (2003)

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH Building 37, Bethesda, MD 20892-4255, USA.

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.

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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.
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Related In: Results  -  Collection


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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.

Mentions: As shown schematically in Figures 1 and 2, MatchMiner leverages information from the four public databases listed above, and from Affymetrix, by parsing them into relational tables for use in doing translations. The LookUp function can operate interactively on single identifiers or in batch mode on a list of identifiers in a file. When used interactively for one or a few genes, it saves the user the trouble of querying five different databases and collating the data. More important, however, is batch querying of a list file, for instance a list of the dozens or hundreds or thousands of genes that show interesting differences between samples in a microarray experiment. In this mode, the user specifies the input and output identifier types, as well as the search algorithms to be used in traversing the various data sources (Table 1). The program is context-sensitive in that it will search only the pertinent data sources (for example, only UniGene to identify IMAGE clone ids, which are not found in the other sources). An important feature is the optional output of diagnostic metadata that tell the user in which source (s) the identifier was found and whether an input identifier corresponds to more than one gene. This feature enables the user to judge the reliability of matches. The results can be displayed in HTML format or downloaded as tab-delimited text suitable for direct entry into a spreadsheet program. A summary indicates the number of successful and unsuccessful translations.


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

Bussey KJ, Kane D, Sunshine M, Narasimhan S, Nishizuka S, Reinhold WC, Zeeberg B, Ajay W, Weinstein JN - Genome Biol. (2003)

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.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC154578&req=5

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.
Mentions: As shown schematically in Figures 1 and 2, MatchMiner leverages information from the four public databases listed above, and from Affymetrix, by parsing them into relational tables for use in doing translations. The LookUp function can operate interactively on single identifiers or in batch mode on a list of identifiers in a file. When used interactively for one or a few genes, it saves the user the trouble of querying five different databases and collating the data. More important, however, is batch querying of a list file, for instance a list of the dozens or hundreds or thousands of genes that show interesting differences between samples in a microarray experiment. In this mode, the user specifies the input and output identifier types, as well as the search algorithms to be used in traversing the various data sources (Table 1). The program is context-sensitive in that it will search only the pertinent data sources (for example, only UniGene to identify IMAGE clone ids, which are not found in the other sources). An important feature is the optional output of diagnostic metadata that tell the user in which source (s) the identifier was found and whether an input identifier corresponds to more than one gene. This feature enables the user to judge the reliability of matches. The results can be displayed in HTML format or downloaded as tab-delimited text suitable for direct entry into a spreadsheet program. A summary indicates the number of successful and unsuccessful translations.

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH Building 37, Bethesda, MD 20892-4255, USA.

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.

Show MeSH