MatchMiner protocols

View MatchMiner computational protocol

MatchMiner statistics

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Associated diseases

Associated diseases

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 Yes


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Publication for MatchMiner

MatchMiner in pipeline

PMCID: 2211756
PMID: 18005444
DOI: 10.1186/1471-2105-8-447

[…] and cross-reference database [] was developed to help investigators identify genes commonly interrogated by different microarray platforms. other software tools such as mergemaid [], genehopper [], matchminer [], and probematchdb [] have been developed for a similar purpose. recent research has demonstrated improved cross-platform correlations when spots are matched by sequence rather […]

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MatchMiner in publications

PMCID: 5428835
PMID: 28373667
DOI: 10.1038/s41598-017-00629-3

[…] incubator with 5% co2 at 37 °c., the prediction of mirnas targeting genes was performed by the algorithms of targetscan, pictar, microrna org and mirwalk targets. the results were intersected by matchminer, suggesting that the nf-κb1/p50 gene was a potential target gene of mir-9., total rna was extracted by trizol or trizol ls reagent from the cells, frozen pancreatic specimens or serum. […]

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

[…] 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., david (the database for annotation, […]

PMCID: 3084815
PMID: 21559394
DOI: 10.1371/journal.pone.0019293

[…] expressed in the colon, seven were not in the pictar database, and mmu-mir-200c* was not in the databases of any of the algorithms employed. to increase the stringency of the prediction, the matchminer program was used to identify target genes that were predicted by at least two algorithms. this bioinformatic approach revealed 164 potentially downregulated target genes […]

PMCID: 3056769
PMID: 21423753
DOI: 10.1371/journal.pone.0017795

[…] official gene symbols. we used affymetrix's mapping of the u133a probe sets to gene symbols. for tango analysis probes were converted to entrez geneid using matchminer . since not all probes capture a recognized gene with an official gene symbol, and some probes capture more than one gene, the actual lengths […]

PMCID: 2996405
PMID: 21070662
DOI: 10.1186/1471-2148-10-351

[…] we decided to provide them with the whole lists. in particular, david recognized 1207 identifiers and mgsa recognized 1101 ids. in addition, overlaps between lists of genes were computed by using matchminer web tool, which also takes into account gene aliases and/or different types of gene identifiers []. this tool recognized 885 schizophrenia, 178 multiple sclerosis, 490 parkinson's disease, […]

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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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