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PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes

Andreas Ruepp1, Andreas Kowarsch, Daniel Schmidl

  • 1Institute for Bioinformatics and Systems Biology (MIPS), Helmholtz Center Munich - German Research Center for Environmental Health (GmbH), Ingolstädter Landstrasse 1, D-85764 Neuherberg, Germany. andreas.ruepp@helmholtz-muenchen.de

Genome Biology
|January 22, 2010
PubMed

Insights

MicroRNAs are crucial in health and disease. Analysis of the PhenomiR database reveals that cell culture findings on microRNA deregulation can differ from those in patient studies, depending on the specific disease.

Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • MicroRNAs (miRNAs) are small non-coding RNAs regulating gene expression.
  • miRNA deregulation is implicated in various physiological and malignant processes.
  • A comprehensive resource is needed to track miRNA expression changes in disease.

Purpose of the Study:

  • To analyze the PhenomiR database, a curated resource of miRNA expression studies.
  • To investigate discrepancies between cell culture and patient studies regarding miRNA deregulation.
  • To highlight the importance of study type in miRNA research.

Main Methods:

  • Systematic curation of data from 542 studies in the PhenomiR database.
  • Comparative analysis of miRNA expression data from cell culture versus patient studies.
  • Disease-specific analysis of miRNA deregulation patterns.

Main Results:

  • The PhenomiR database contains manually curated data on miRNA deregulation across 542 studies.
  • Analysis revealed that conclusions from cell culture studies often contrast with those from patient studies.
  • These discrepancies are dependent on the specific disease context.

Conclusions:

  • MicroRNA expression patterns in cell cultures may not always reflect in vivo disease states.
  • Careful consideration of study type (cell culture vs. patient) is essential for interpreting miRNA research.
  • The PhenomiR database serves as a valuable resource for understanding miRNA roles in disease.

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