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Inference of circadian regulatory networks

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

We assess the accuracy of various state-of-the-art methods for reconstructing gene and protein regulatory networks in the context of circadian regulation. Gene expression and protein concentration time series are simulated from a recently published regulatory network of the circadian clock in A. thaliana, which is mathematically described by a Markov jump process based on Michaelis-Menten kinetics. Our study provides relative network reconstruction accuracy scores for a critical comparative performance evaluation, quantifies the influence of systematically missing values related to unknown protein concentrations and
mRNA transcription rates, and investigates the dependence of the performance
on the network topology and the degree of recurrency. An application to recent gene expression time series from qPCR experiments suggests new hypotheses about the structure of the central circadian gene regulatory network in A. thaliana.

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Original languageEnglish
Title of host publicationProceedings of the 2nd International Work-Conference on Bioinformatics and Biomedical Engineering
PublisherCopicentro Granada S L
Pages1001-1014
ISBN (Print)978-84-15814-84-9
Publication statusPublished - 2014
EventIWBBIO 2014 2nd International Work-Conference on Bioinformatics and Biomedical Engineering - Science Faculty of the University of Granada, Granada, Spain
Duration: 7 Apr 20149 Apr 2014

Conference

ConferenceIWBBIO 2014 2nd International Work-Conference on Bioinformatics and Biomedical Engineering
CountrySpain
CityGranada
Period7/04/149/04/14

    Research areas

  • Regulatory network inference, Circadian clock, ANOVA

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ID: 181068843