Journal
NUCLEIC ACIDS RESEARCH
Volume 41, Issue W1, Pages W159-W164Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkt379
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Funding
- National Institutes of Health (NIH) - National Library of Medicine (NLM) [LM007994, LM009657]
- Fondazione Ri.MED
- NIH - NLM [LM009657]
- Direct For Biological Sciences
- Division Of Integrative Organismal Systems [1024811] Funding Source: National Science Foundation
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ComiR is a web tool for combinatorial microRNA (miRNA) target prediction. Given an messenger RNA (mRNA) in human, mouse, fly or worm genomes, ComiR computes the potential of being targeted by a set of miRNAs, each of which can have zero, one or more targets on its 3'untranslated region. In determining the regulatory potential of an mRNA from a set of miRNAs, ComiR uses user-provided miRNA expression levels in a combination of appropriate thermodynamic modeling and machine learning techniques to make more accurate predictions. For each gene, ComiR returns the probability of being a functional target of a set of miRNAs, which depends on the relative miRNA expression levels. The tool provides a user-friendly interface to input a miRNA expression table containing many sample information and filter out the most relevant miRNAs. ComiR results can be downloaded or visualized on a table, which can then be used to select the most relevant targets and to compare the results obtained with different miRNA expression input. ComiR is freely available for academic use at http://www.benoslab.pitt.edu/comir/.
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