TitleRandomization Strategies Affect Motif Significance Analysis in TF-miRNA-Gene Regulatory Networks
Publication TypeJournal Article
Year of Publication2017
AuthorsSadegh, S., M. Nazarieh, C. Spaniol, and V. Helms
JournalJ. Integr. Bioinform
Volume14 (2)
KeywordsFeed-forward loop; Network randomization; Target gene; Transcription factor; Transcriptional regulation

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.














  Legal notice Privacy policy