PMID- 28911111
OWN - NLM
STAT- In-Process
DA  - 20170915
LR  - 20170917
IS  - 1362-4962 (Electronic)
IS  - 0305-1048 (Linking)
VI  - 45
IP  - 15
DP  - 2017 Sep 06
TI  - Combinatorial ensemble miRNA target prediction of co-regulation networks with
      non-prediction data.
PG  - 8745-8757
LID - 10.1093/nar/gkx605 [doi]
AB  - MicroRNAs (miRNAs) are key regulators of cell-fate decisions in development and
      disease with a vast array of target interactions that can be investigated using
      computational approaches. For this study, we developed metaMIR, a combinatorial
      approach to identify miRNAs that co-regulate identified subsets of genes from a
      user-supplied list. We based metaMIR predictions on an improved dataset of human 
      miRNA-target interactions, compiled using a machine-learning-based meta-analysis 
      of established algorithms. Simultaneously, the inverse dataset of negative
      interactions not likely to occur was extracted to increase classifier
      performance, as measured using an expansive set of experimentally validated
      interactions from a variety of sources. In a second differential mode, candidate 
      miRNAs are predicted by indicating genes to be targeted and others to be avoided 
      to potentially increase specificity of results. As an example, we investigate the
      neural crest, a transient structure in vertebrate development where miRNAs play a
      pivotal role. Patterns of metaMIR-predicted miRNA regulation alone partially
      recapitulated functional relationships among genes, and separate differential
      analysis revealed miRNA candidates that would downregulate components implicated 
      in cancer progression while not targeting tumour suppressors. Such an approach
      could aid in therapeutic application of miRNAs to reduce unintended effects. The 
      utility is available at http://rna.informatik.uni-freiburg.de/metaMIR/.
CI  - (c) The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic
      Acids Research.
FAU - Davis, Jason A
AU  - Davis JA
AD  - Department of Molecular Embryology, Institute of Anatomy and Cell Biology,
      Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.
FAU - Saunders, Sita J
AU  - Saunders SJ
AD  - Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University
      Freiburg, Georges-Kohler-Allee 106, 79110 Freiburg, Germany.
FAU - Mann, Martin
AU  - Mann M
AD  - Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University
      Freiburg, Georges-Kohler-Allee 106, 79110 Freiburg, Germany.
FAU - Backofen, Rolf
AU  - Backofen R
AD  - Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University
      Freiburg, Georges-Kohler-Allee 106, 79110 Freiburg, Germany.
AD  - ZBSA Centre for Biological Systems Analysis, Albert-Ludwigs-University Freiburg, 
      Habsburgerstr. 49, 79104 Freiburg, Germany.
AD  - BIOSS Centre for Biological Signalling Studies, Cluster of Excellence,
      Albert-Ludwigs-University Freiburg, Germany.
AD  - Centre for non-coding RNA in Technology and Health, University of Copenhagen, Gr 
      solidus in circlennegardsvej 3, DK-1870 Frederiksberg C, Denmark.
LA  - eng
PT  - Journal Article
PL  - England
TA  - Nucleic Acids Res
JT  - Nucleic acids research
JID - 0411011
PMC - PMC5587804
EDAT- 2017/09/16 06:00
MHDA- 2017/09/16 06:00
CRDT- 2017/09/16 06:00
PHST- 2016/11/24 [received]
PHST- 2017/07/06 [accepted]
AID - 3958712 [pii]
AID - 10.1093/nar/gkx605 [doi]
PST - ppublish
SO  - Nucleic Acids Res. 2017 Sep 6;45(15):8745-8757. doi: 10.1093/nar/gkx605.