title: Regulatory network of microRNAs in RAW 264.7 macrophage cells.
abstract: microRNAs (miRNA) play important roles in regulating immunity. Here we utilize the systems biology approach to predict the regulatory network of miRNAs among the most down-regulated genes by the lipopolysaccharides (LPS) treatment in the macrophage RAW267.4 cell line. We combine the proteome and transcriptome data sets to define 200 target genes that are significantly down-regulated by the LPS treatment. We perform the profiling of over 300 miRNAs with the RNA-Seq method. Using the complementary binding rule between the seed sequences of profiled miRNAs and the 3'UTRs of target genes, we predict genes involved in mobility, metabolism, and oxidative phosphorylation as the top targets of miRNA negative regulation.
authors.affiliation: Bioengineering Department of UC-San Diego, La Jolla, USA. lgarmire@ucsd.edu
authors.forename: Lana X
authors.initials: LX
authors.lastname: Garmire
authors.forename: Zhouxin
authors.initials: Z
authors.lastname: Shen
authors.forename: Steve
authors.initials: S
authors.lastname: Briggs
authors.forename: Gene
authors.initials: G
authors.lastname: Yeo
authors.forename: Shankar
authors.initials: S
authors.lastname: Subramaniam
authors.forename: Christopher
authors.initials: C
authors.lastname: Glass
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D000818:Animals; D015536:Down-Regulation / Q000187:drug effects; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks / Q000187:drug effects; D008070:Lipopolysaccharides / Q000494:pharmacology; D008264:Macrophages / Q000187:drug effects / Q000378:metabolism*; D051379:Mice; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D020543:Proteome / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism
chemical_list: D020413:3' Untranslated Regions; D008070:Lipopolysaccharides; D035683:MicroRNAs; D020543:Proteome; D012333:RNA, Messenger