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Refining Regulatory Networks through Phylogenetic Transfer of Information
July-Aug. 2012 (vol. 9 no. 4)
pp. 1032-1045
ASCII Text
x 
 
Xiuwei Zhang, B. M. E. Moret, "Refining Regulatory Networks through Phylogenetic Transfer of Information," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 4, pp. 1032-1045, July-Aug., 2012.
 
 
BibTex
x
 
@article{ 10.1109/TCBB.2012.62,
author = { Xiuwei Zhang and B. M. E. Moret},
title = {Refining Regulatory Networks through Phylogenetic Transfer of Information},
journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
volume = {9},
number = {4},
issn = {1545-5963},
year = {2012},
pages = {1032-1045},
doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2012.62},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - JOUR
JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics
TI - Refining Regulatory Networks through Phylogenetic Transfer of Information
IS - 4
SN - 1545-5963
SP1032
EP1045
EPD - 1032-1045
A1 - Xiuwei Zhang,
A1 - B. M. E. Moret,
PY - 2012
KW - probability
KW - bioinformatics
KW - biological techniques
KW - complex networks
KW - evolution (biological)
KW - genetics
KW - inference mechanisms
KW - evolutionary information
KW - regulatory network refinement
KW - phylogenetic information transfer
KW - transcriptional regulatory networks
KW - single organism approach
KW - computational biology
KW - ProPhyC
KW - probabilistic phylogenetic model
KW - inference algorithms
KW - regulatory network inference
KW - evolutionary relationships
KW - network evolutionary models
KW - transfer learning approach
KW - Computational modeling
KW - Phylogeny
KW - Biological system modeling
KW - Inference algorithms
KW - Vegetation
KW - Algorithm design and analysis
KW - Organisms
KW - transfer learning.
KW - Regulatory networks
KW - network inference
KW - evolution
KW - phylogenetic relationships
KW - ancestral network
KW - refinement
KW - gene duplication
KW - evolutionary model
KW - evolutionary history
KW - reconciliation
KW - maximum likelihood
VL - 9
JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics
ER -
 
Xiuwei Zhang, Lab. for Comput. Biol. & Bioinf., Ecole Polytech. Fed. de Lausanne, Lausanne, Switzerland
B. M. E. Moret, Lab. for Comput. Biol. & Bioinf., Ecole Polytech. Fed. de Lausanne, Lausanne, Switzerland
The experimental determination of transcriptional regulatory networks in the laboratory remains difficult and time-consuming, while computational methods to infer these networks provide only modest accuracy. The latter can be attributed partly to the limitations of a single-organism approach. Computational biology has long used comparative and evolutionary approaches to extend the reach and accuracy of its analyses. In this paper, we describe ProPhyC, a probabilistic phylogenetic model and associated inference algorithms, designed to improve the inference of regulatory networks for a family of organisms by using known evolutionary relationships among these organisms. ProPhyC can be used with various network evolutionary models and any existing inference method. Extensive experimental results on both biological and synthetic data confirm that our model (through its associated refinement algorithms) yields substantial improvement in the quality of inferred networks over all current methods. We also compare ProPhyC with a transfer learning approach we design. This approach also uses phylogenetic relationships while inferring regulatory networks for a family of organisms. Using similar input information but designed in a very different framework, this transfer learning approach does not perform better than ProPhyC, which indicates that ProPhyC makes good use of the evolutionary information.

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Index Terms:
probability,bioinformatics,biological techniques,complex networks,evolution (biological),genetics,inference mechanisms,evolutionary information,regulatory network refinement,phylogenetic information transfer,transcriptional regulatory networks,single organism approach,computational biology,ProPhyC,probabilistic phylogenetic model,inference algorithms,regulatory network inference,evolutionary relationships,network evolutionary models,transfer learning approach,Computational modeling,Phylogeny,Biological system modeling,Inference algorithms,Vegetation,Algorithm design and analysis,Organisms,transfer learning.,Regulatory networks,network inference,evolution,phylogenetic relationships,ancestral network,refinement,gene duplication,evolutionary model,evolutionary history,reconciliation,maximum likelihood
Citation:
Xiuwei Zhang, B. M. E. Moret, "Refining Regulatory Networks through Phylogenetic Transfer of Information," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 4, pp. 1032-1045, July-Aug. 2012, doi:10.1109/TCBB.2012.62
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