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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Entropic Biological Score: a cell cycle investigation for GRNs inference

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Author(s):
Lopes, Fabricio M. [1] ; Ray, Shubhra Sankar [2, 3] ; Hashimoto, Ronaldo F. [4] ; Cesar, Jr., Roberto M. [4]
Total Authors: 4
Affiliation:
[1] Fed Univ Technol, Curitiba, Parana - Brazil
[2] Indian Stat Inst, Ctr Soft Comp Res, Kolkata 700108 - India
[3] Indian Stat Inst, Machine Intelligence Unit, Kolkata 700108 - India
[4] Univ Sao Paulo, Inst Math & Stat, BR-05508 Sao Paulo - Brazil
Total Affiliations: 4
Document type: Journal article
Source: Gene; v. 541, n. 2, p. 129-137, MAY 15 2014.
Web of Science Citations: 14
Abstract

Inference of gene regulatory networks (GRNs) is one of the most challenging research problems of Systems Biology. In this investigation, a new GRNs inference methodology, called Entropic Biological Score (EBS), which linearly combines the mean conditional entropy (MCE) from expression levels and a Biological Score (BS), obtained by integrating different biological data sources, is proposed. The EBS is validated with the Cell Cycle related functional annotation information, available from Munich Information Center for Protein Sequences (MIPS), and compared with some existing methods like MRNET, ARACNE, CLR and MCE for GRNs inference. For real networks, the performance of EBS, which uses the concept of integrating different data sources, is found to be superior to the aforementioned inference methods. The best results for EBS are obtained by considering the weights w(1) = 0.2 and w(2) = 0.8 for MCE and BS values, respectively, where approximately 40% of the inferred connections are found to be correct and significantly better than related methods. The results also indicate that expression profile is able to recover some true connections, that are not present in biological annotations, thus leading to the possibility of discovering new relations between its genes. (C) 2014 Elsevier B.V. All rights reserved. (AU)

FAPESP's process: 11/50761-2 - Models and methods of e-Science for life and agricultural sciences
Grantee:Roberto Marcondes Cesar Junior
Support Opportunities: Research Projects - Thematic Grants
FAPESP's process: 10/52138-8 - Data integration in systems biology: characterization of biological phenomena from structural and functional information
Grantee:Ronaldo Fumio Hashimoto
Support Opportunities: Regular Research Grants