D158–D162 Nucleic Acids Research, 2011, Vol. 39, Database issue doi:10.1093/nar/gkq1094 Published online 9 November 2010 miRGator v2.0 : an integrated system for functional investigation of microRNAs Sooyoung Cho 1 , Yukyung Jun 1 , Sanghyun Lee 1 , Hyung-Seok Choi1, Sungchul Jung 1 , Youngjun Jang 2 , Charny Park1, Sangok Kim1, Sanghyuk Lee1,2,* and Wankyu Kim1,* 1Ewha Research Center for Systems Biology (ERCSB), Ewha Womans University, 11-1 Daehyun-dong, Seodaemun-gu, Seoul 120-750 and 2Korean Bioinformation Center (KOBIC), 52 Eoeun-dong, Yuseong-gu, Daejeon, 305-806, KOREA Received September 15, 2010; Revised October 14, 2010; Accepted October 15, 2010 ABSTRACT miRGator is an integrated database of microRNA (miRNA)-associated gene expression, target predic- tion, disease association and genomic annotation, which aims to facilitate functional investigation of miRNAs. The recent version of miRGator v2.0 contains information about (i) human miRNA expres- sion profiles under various experimental conditions, (ii) paired expression profiles of both mRNAs and miRNAs, (iii) gene expression profiles under miRNA-perturbation (e.g. miRNA knockout and overexpression), (iv) known/predicted miRNA targets and (v) miRNA-disease associations. In total, >8000 miRNA expression profiles, 300 miRNA-perturbed gene expression profiles and 2000 mRNA expression profiles are compiled with manually curated annotations on disease, tissue type and perturbation. By integrating these data sets, a series of novel associations (miRNA– miRNA, miRNA–disease and miRNA–target) is extracted via shared features. For example, differ- entially expressed genes (DEGs) after miRNA knockout were systematically compared against miRNA targets. Likewise, differentially expressed miRNAs (DEmiRs) were compared with disease-associated miRNAs. Additionally, miRNA expression and disease-phenotype profiles revealed miRNA pairs whose expression was regulated in parallel in various experimental and disease conditions. Complex associations are readily accessible using an interactive network visu- alization interface. The miRGator v2.0 serves as a reference database to investigate miRNA expres- sion and function (http://miRGator.kobic.re.kr). INTRODUCTION MicroRNAs (miRNAs) are important post- transcriptional regulators that are associated with various cell functions and human diseases. MiRNAs bind to complementary sequences in the 30 UTRs of target mRNAs resulting in negative regulation of gene expression (1,2). Signiﬁcant efforts have been made to study the function of miRNAs and their target genes. However, the function of most miRNAs are still elusive and under active investigation. A number of miRNA-related databases have been developed. There are many miRNA target prediction algorithms available including TargetScan (3), PITA (4), miRanda (5), PicTar (6), miBridge (7) and many more. PhenomiR (8) and miR2Disease (9) provide information on disease- associated miRNAs from literature curation. FAME (10) uses a target prediction method to infer biological processes affected by human miRNAs. MMIA (11) and MAGIA (12) provide tools for gene (or miRNA) set analysis and target prediction using miRNA–miRNA ex- pression proﬁles. MiRGator is an integrated database of miRNA- associated gene expression, target prediction, disease asso- ciation and genomic annotation, which aims to facilitate functional investigation of miRNAs. In this update version, we integrate a variety of publicly available data sets related to miRNA biology. Overall, more than 10 000 miRNA/mRNA expression proﬁles are compiled and organized by manual curation according to miRNA, tissue type, disease and perturbation. MiRGator contains information about (i) human miRNA expression proﬁles under various experimental conditions, (ii) paired expression proﬁles of both mRNAs and miRNAs from the same sample, (iii) gene expression proﬁles under miRNA- perturbation (e.g. miRNA knockout and overexpression), (iv) known/predicted miRNA targets and (v) miRNA- disease associations. In addition, a number of new *To whom correspondence should be addressed. Tel: +82 2 3277 2888; Fax: +82 2 3277 3760; Email: sanghyuk@ewha.ac.kr Correspondence may also be addressed to Wankyu Kim. Tel: +82 2 3277 4132; Fax: +82 2 3277 6809; Email: wkim@ewha.ac.kr The authors wish it to be known that, in their opinion, the ﬁrst three authors should be regarded as joint First Authors. The Author(s) 2010. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.