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MatchMiner specifications


Unique identifier OMICS_18325
Name MatchMiner
Interface Web user interface
Restrictions to use None
Input data A list of gene identifiers.
Output data A list of identifiers of a different type.
Computer skills Basic
Stability Stable
Maintained No


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Publication for MatchMiner

MatchMiner citations


Integrated DNA Copy Number and Gene Expression Regulatory Network Analysis of Non small Cell Lung Cancer Metastasis

Cancer Inform
PMCID: 4218678
PMID: 25392690
DOI: 10.4137/CIN.S14055

[…] hromosomal location of each probe and its copy number value. There is no chromosomal information of genes in GE datasets, requiring the use of some public repositories such as UCSC Genome Browser and MatchMiner. To find the chromosomal location for each gene, gene names should be entered to the software in a batch mode, and the output includes chromosomal location. The DNA copy number probes must […]


Colonic miRNA Expression/Secretion, Regulated by Intestinal Epithelial PepT1, Plays an Important Role in Cell to Cell Communication during Colitis

PLoS One
PMCID: 3929505
PMID: 24586284
DOI: 10.1371/journal.pone.0087614

[…] et prediction algorithms were used: PicTar ( , MicroCosm ( and TargetScan ( . The Matchminer program ( ner/index.jsp) was then used to determine genes that were identified by at least two algorithms. […]


Overview of biological database mapping services for interoperation between different 'omics' datasets

Hum Genomics
PMCID: 3525252
PMID: 22155608
DOI: 10.1186/1479-7364-5-6-703

[…] ication programming interface (API) for programmatic access, as well as file transfer protocol (FTP) downloads if the user wishes to have a local Id mapping service for large datasets (> 100,000 Ids).MatchMiner[] is tool that provides a clean interface with an interesting BatchMerge option, along with Interactive Lookup and Batch Lookup. Interactive Lookup and Batch Lookup can be used for generic […]


The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services

BMC Bioinformatics
PMCID: 2824678
PMID: 20047655
DOI: 10.1186/1471-2105-11-5

[…] one set correspond to which identifiers in the other set.This problem of identifier mapping has been recognized, and a number of resources have been developed to solve it, including DICT[], CRONOS[], MatchMiner[], AliasServer[], PICR[], Synergizer[] and Ensembl BioMart[]. For the most part, these resources accurately map identifiers and provide an interface, usually a web site, to the mappings. Ho […]


Post Translational Regulation of Oct4 Transcriptional Activity

PLoS One
PMCID: 2637973
PMID: 19221599
DOI: 10.1371/journal.pone.0004467

[…] revious studies, gene identifiers were downloaded and pooled from supplemental data lists, and converted to common identifiers using the DAVID gene ID conversion tool (, Matchminer utility (; ) and WebGestalt Gene Set Analysis Toolkit (; ). Multiple conversions were performed to en […]


Bioinformatic Tools for Inferring Functional Information from Plant Microarray Data: Tools for the First Steps

Int J Plant Genomics
PMCID: 2408683
PMID: 18528524
DOI: 10.1155/2008/147563

[…] MatchMiner translates between several gene identifier types for the same list of hundreds or thousands of genes. The gene identifier types supported by the tool includes GenBank accession numbers, IMA […]


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MatchMiner institution(s)
Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA; SRA International Inc., Fairfax, VA, USA

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