PhenomiR statistics

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Citations per year

Number of citations per year for the bioinformatics software tool PhenomiR

Tool usage distribution map

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Associated diseases


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PhenomiR specifications


Unique identifier OMICS_02825
Name PhenomiR
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 2.0
Maintained Yes


  • Primates
    • Homo sapiens


  • person_outline Andreas Ruepp

Publications for PhenomiR

PhenomiR citations


Identifying miRNA sponge modules using biclustering and regulatory scores

BMC Bioinformatics
PMCID: 5374547
PMID: 28361682
DOI: 10.1186/s12859-017-1467-5

[…] rom COSMIC v77 [], GAD [], OMIM [], BCGD [] and G2SBC []. The list of 428 breast cancer miRNAs are obtained by integrating five databases: HMDD v2.0 [], miR2Disease [], miRCancer [], oncomiRDB [] and phenomiR v2.0 [].The experimentally validated miRNA-target interactions with strong evidence are from miRTarbase v6.1 []. The experimentally validated miRNA sponge interactions are retrived from [, ], […]


Anomalous altered expressions of downstream gene targets in TP53 miRNA pathways in head and neck cancer

Sci Rep
PMCID: 5385823
PMID: 25186767
DOI: 10.1038/srep06280

[…] To build up the TP53-miRNA network, manually curated TP53 controlled miRNAs from the TF-miRNA regulation database, TransmiR, were assembled. The HNSCC databases, HNOCDB and PhenomiR2, containing differentially regulated miRNA expression in diseases and other biological processes, were used for corroboration, and further extended this network by extracting validated miRNA […]


The Potential of MicroRNAs in Personalized Medicine against Cancers

Biomed Res Int
PMCID: 4163464
PMID: 25243170
DOI: 10.1155/2014/642916

[…] th (lipo)proteins (HDL and Argonaute 2) [–].Similar to mutations, several miRNA profiles in various human specimens and cancers have been collected and made publicly available in dedicated databases: PhenomiR [], oncomiRDB [], PROGmiR [], miRò [], and miRandola []. We acknowledge that revisiting these data can dampen enthusiasm for the diagnostic/prognostic potential of miRNAs [, ]. In fact, no ma […]


Exploration of miRNA families for hypotheses generation

Sci Rep
PMCID: 3796740
PMID: 24126940
DOI: 10.1038/srep02940

[…] ng miRNA function are based on the interaction of mature miRNA and mRNA, and not on miRNA family groups. The function of mature miRNA in model species, such as human and mouse, has been well studied. PhenomiR, miRdSNB, HMDD, miRNAMap and miRBase (see “Methods”) provide useful links of the functional mature miRNA to their genes and associated diseases, but do not associate miRNA and miRNA gene char […]


In Silico Algorithms for the Screening of Possible microRNA Binding Sites and Their Interactions

Curr Genomics
PMCID: 3637677
PMID: 24082822
DOI: 10.2174/1389202911314020005

[…] eatment of diseases by miRNA (s). The information on cell lines related to specific miRNA(s), diseases, and gene(s) can be easily retrieved from miRWalk [], TarBase [], miRTarBase [], miR2Disease [], PhenomiR [] and HMDD []. Afterwards, these cell lines can be used to measure the expressions of one or more predicted miRNAs and/or genes under different pathophysiological conditions. Recently, Anger […]

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PhenomiR institution(s)
Institute for Bioinformatics and Systems Biology (MIPS), Helmholtz Zentrum München, Germany; Research Center for Environmental Health, Neuherberg, Germany
PhenomiR funding source(s)
Supported by the Federal Ministry of Education and Research (BMBF), its MedSys initiative (projects LungSys and SysMBo), the Helmholtz Alliance on Systems Biology (project CoReNe), and the German Research Foundation (InKoMBio, SPP1395).

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