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BRANE Clust: Cluster-Assisted Gene Regulatory Network Inference Refinement

View ORCID ProfileAurélie Pirayre, Camille Couprie, View ORCID ProfileLaurent Duval, Jean-Christophe Pesquet
doi: https://doi.org/10.1101/114769
Aurélie Pirayre
aIFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France. E-mail:
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  • ORCID record for Aurélie Pirayre
  • For correspondence: aurelie.pirayre@ifpen.fr
Camille Couprie
bFacebook AI Research, Paris, France.
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Laurent Duval
aIFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France. E-mail:
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  • For correspondence: aurelie.pirayre@ifpen.fr
Jean-Christophe Pesquet
cCentraleSupélec France.
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Abstract

Discovering meaningful gene interactions is crucial for the identification of novel regulatory processes in cells. Building accurately the related graphs remains challenging due to the large number of possible solutions from available data. Nonetheless, enforcing a priori on the graph structure, such as modularity, may reduce network indeterminacy issues. BRANE Clust (Biologically-Related A priori Network Enhancement with Clustering) refines gene regulatory network (GRN) inference thanks to cluster information. It works as a post-processing tool for inference methods (i.e. CLR, GENIE3). In BRANE Clust, the clustering is based on the inversion of a system of linear equations involving a graph-Laplacian matrix promoting a modular structure. Our approach is validated on DREAM4 and DREAM5 datasets with objective measures, showing significant comparative improvements. We provide additional insights on the discovery of novel regulatory or co-expressed links in the inferred Escherichia coli network evaluated using the STRING database. The comparative pertinence of clustering is discussed computationally (SIMoNe, WGCNA, X-means) and biologically (RegulonDB). BRANE Clust software is available at: http://www-syscom.univ-mlv.fr/∼pirayre/Codes-GRN-BRANE-clust.html

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Posted March 24, 2017.
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BRANE Clust: Cluster-Assisted Gene Regulatory Network Inference Refinement
Aurélie Pirayre, Camille Couprie, Laurent Duval, Jean-Christophe Pesquet
bioRxiv 114769; doi: https://doi.org/10.1101/114769
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BRANE Clust: Cluster-Assisted Gene Regulatory Network Inference Refinement
Aurélie Pirayre, Camille Couprie, Laurent Duval, Jean-Christophe Pesquet
bioRxiv 114769; doi: https://doi.org/10.1101/114769

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