title: RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse.
abstract: Transcriptional and post-transcriptional regulation of gene expression is of fundamental importance to numerous biological processes. Nowadays, an increasing amount of gene regulatory relationships have been documented in various databases and literature. However, to more efficiently exploit such knowledge for biomedical research and applications, it is necessary to construct a genome-wide regulatory network database to integrate the information on gene regulatory relationships that are widely scattered in many different places. Therefore, in this work, we build a knowledge-based database, named 'RegNetwork', of gene regulatory networks for human and mouse by collecting and integrating the documented regulatory interactions among transcription factors (TFs), microRNAs (miRNAs) and target genes from 25 selected databases. Moreover, we also inferred and incorporated potential regulatory relationships based on transcription factor binding site (TFBS) motifs into RegNetwork. As a result, RegNetwork contains a comprehensive set of experimentally observed or predicted transcriptional and post-transcriptional regulatory relationships, and the database framework is flexibly designed for potential extensions to include gene regulatory networks for other organisms in the future. Based on RegNetwork, we characterized the statistical and topological properties of genome-wide regulatory networks for human and mouse, we also extracted and interpreted simple yet important network motifs that involve the interplays between TF-miRNA and their targets. In summary, RegNetwork provides an integrated resource on the prior information for gene regulatory relationships, and it enables us to further investigate context-specific transcriptional and post-transcriptional regulatory interactions based on domain-specific experimental data. Database URL: http://www.regnetworkweb.org.
authors.affiliation: Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong 250061, China and.
authors.forename: Zhi-Ping
authors.initials: ZP
authors.lastname: Liu
authors.affiliation: Department of Biostatistics, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
authors.forename: Canglin
authors.initials: C
authors.lastname: Wu
authors.affiliation: Department of Biostatistics, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
authors.forename: Hongyu
authors.initials: H
authors.lastname: Miao
authors.affiliation: Department of Biostatistics, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA Hulin.Wu@uth.tmc.edu.
authors.forename: Hulin
authors.initials: H
authors.lastname: Wu
mesh_terms: D000818:Animals; D030541:Databases, Genetic; D005786:Gene Expression Regulation / Q000502:physiology*; D053263:Gene Regulatory Networks / Q000502:physiology*; D006801:Humans; D051188:Knowledge Bases; D051379:Mice; D035683:MicroRNAs / Q000096:biosynthesis / Q000235:genetics; D059372:Nucleotide Motifs; D020218:Response Elements / Q000502:physiology*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic / Q000502:physiology*
chemical_list: D035683:MicroRNAs; D014157:Transcription Factors