title: STarMirDB: A database of microRNA binding sites.
abstract: microRNAs (miRNAs) are an abundant class of small endogenous non-coding RNAs (ncRNAs) of ∼22 nucleotides (nts) in length. These small regulatory molecules are involved in diverse developmental, physiological and pathological processes. miRNAs target mRNAs (mRNAs) for translational repression and/or mRNA degradation. Predictions of miRNA binding sites facilitate experimental validation of miRNA targets. Models developed with data from CLIP studies have been used for predictions of miRNA binding sites in the whole transcriptomes of human, mouse and worm. The prediction results have been assembled into STarMirDB, a new database of miRNA binding sites available at http://sfold.wadsworth.org/starmirDB.php . STarMirDB can be searched by miRNAs or mRNAs separately or in combination. The search results are categorized into seed and seedless sites in 3' UTR, CDS and 5' UTR. For each predicted site, STarMirDB provides a comprehensive list of sequence, thermodynamic and target structural features that are known to influence miRNA: target interaction. A high resolution PDF diagram of the conformation of the miRNA:target hybrid is also available for visualization and publication. The results of a database search are available through both an interactive viewer and downloadable text files.
authors.affiliation: a Wadsworth Center, New York State Department of Health , Center for Medical Science , Albany , NY , USA.
authors.forename: William
authors.initials: W
authors.lastname: Rennie
authors.affiliation: a Wadsworth Center, New York State Department of Health , Center for Medical Science , Albany , NY , USA.
authors.forename: Shaveta
authors.initials: S
authors.lastname: Kanoria
authors.affiliation: a Wadsworth Center, New York State Department of Health , Center for Medical Science , Albany , NY , USA.
authors.forename: Chaochun
authors.initials: C
authors.lastname: Liu
authors.affiliation: a Wadsworth Center, New York State Department of Health , Center for Medical Science , Albany , NY , USA.
authors.forename: Bibekanand
authors.initials: B
authors.lastname: Mallick
authors.affiliation: a Wadsworth Center, New York State Department of Health , Center for Medical Science , Albany , NY , USA.
authors.forename: Dang
authors.initials: D
authors.lastname: Long
authors.affiliation: a Wadsworth Center, New York State Department of Health , Center for Medical Science , Albany , NY , USA.
authors.forename: Adam
authors.initials: A
authors.lastname: Wolenc
authors.affiliation: a Wadsworth Center, New York State Department of Health , Center for Medical Science , Albany , NY , USA.
authors.forename: C Steven
authors.initials: CS
authors.lastname: Carmack
authors.affiliation: a Wadsworth Center, New York State Department of Health , Center for Medical Science , Albany , NY , USA.
authors.forename: Jun
authors.initials: J
authors.lastname: Lu
authors.affiliation: a Wadsworth Center, New York State Department of Health , Center for Medical Science , Albany , NY , USA.
authors.forename: Ye
authors.initials: Y
authors.lastname: Ding
mesh_terms: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D000818:Animals; D001665:Binding Sites; D017173:Caenorhabditis elegans / Q000235:genetics*; D030561:Databases, Nucleic Acid; D005786:Gene Expression Regulation; D006801:Humans; D051379:Mice; D035683:MicroRNAs / Q000235:genetics*; D020871:RNA Stability; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics*; D017423:Sequence Analysis, RNA; D012984:Software; D014584:User-Computer Interface
chemical_list: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D035683:MicroRNAs; D012333:RNA, Messenger
keywords: Binding site prediction; CLIP; microRNA; seed site; seedless site