An integrated gene regulatory network inference pipeline

Rapidly accumulated gene expression data put forward the development of numerous methods for inferring gene regulatory networks and the efforts for critical performance assessment of these methods. In this paper, we propose an integrated pipeline for gene regulatory network inference motivated by th...

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Bibliographic Details
Published in:Proceedings of the 30th Chinese Control Conference pp. 6593 - 6598
Main Authors: Wang Yong, Katsuhisa, Horimoto, Chen Luonan
Format: Conference Proceeding
Language:English
Published: IEEE 01.07.2011
Subjects:
Correlation
Equations
Gene expression
Gene regulatory network
Knock out
Mathematical model
Mutual information
Pipelines
Reverse engineering
Steady state
Time series
ISBN:9781457706776, 1457706776
ISSN:1934-1768
Online Access:Get full text
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Summary:Rapidly accumulated gene expression data put forward the development of numerous methods for inferring gene regulatory networks and the efforts for critical performance assessment of these methods. In this paper, we propose an integrated pipeline for gene regulatory network inference motivated by the results and follow-up analysis of a blinded, community-wide challenge DREAM (Dialogue on Reverse Engineering Assessment and Methods) project. In particular, we categorize the gene expression data into three types, i.e., steady-state gene expression profile of knockout or knockdown experiments, steady-state gene expression profiles after multi-factorial perturbations, and time-series data after multi-factorial perturbations. Then we analyze the three types of gene expression data by using the combination of fold change and t-test, the path consistency algorithm based on conditional mutual information, and the ordinary differential equation model, respectively. Finally we integrate the three procedures to a pipeline for gene regulatory network inference by considering their complementarities. Performance for the network inference will be improved in the proposed pipeline by maximally utilizing information in the available data, emphasizing the knock-out and knock-down data, and differentiating the direct and indirect regulatory interactions.
ISBN:9781457706776
1457706776
ISSN:1934-1768