Please use this identifier to cite or link to this item: doi:10.22028/D291-30519
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Title: Randomization Strategies Affect Motif Significance Analysis in TF-miRNA-Gene Regulatory Networks
Author(s): Sadegh, Sepideh
Nazarieh, Maryam
Spaniol, Christian
Helms, Volkhard
Language: English
Title: Journal of integrative bioinformatics : JIB
Volume: 14
Issue: 2
Startpage: 1
Endpage: 11
Publisher/Platform: De Gruyter
Year of Publication: 2017
Publikation type: Journal Article
Abstract: Gene-regulatory networks are an abstract way of capturing the regulatory connectivity between transcription factors, microRNAs, and target genes in biological cells. Here, we address the problem of identifying enriched co-regulatory three-node motifs that are found significantly more often in real network than in randomized networks. First, we compare two randomization strategies, that either only conserve the degree distribution of the nodes' in- and out-links, or that also conserve the degree distributions of different regulatory edge types. Then, we address the issue how convergence of randomization can be measured. We show that after at most 10 × |E| edge swappings, converged motif counts are obtained and the memory of initial edge identities is lost.
DOI of the first publication: 10.1515/jib-2017-0017
URL of the first publication: https://www.degruyter.com/view/j/jib.2017.14.issue-2/jib-2017-0017/jib-2017-0017.xml
Link to this record: hdl:20.500.11880/28895
http://dx.doi.org/10.22028/D291-30519
ISSN: 1613-4516
1432-4385
Date of registration: 20-Mar-2020
Faculty: NT - Naturwissenschaftlich- Technische Fakultät
Department: NT - Biowissenschaften
Professorship: NT - Prof. Dr. Volkhard Helms
Collections:UniBib – Die Universitätsbibliographie

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