features have been added to the previous version, such as association analysis among miRNAs, diseases and per- turbations and an integrated network viewer. Here, an overview of the miRGator system, the collection and pro- cessing of data sets, and important features are brieﬂy described. A more detailed usage and documentation are provided on-line (http://miRGator.kobic.re.kr). SYSTEM OVERVIEW The miRGator v2.0 consists of three main modules: the data set browser, the association analysis and the gene set analysis (GSA)/miRNA set analysis (miRSA) modules. The overall system of miRGator v2.0 is shown in Figure 1. Each of these three modules has its distinct function but they are tightly integrated to facilitate func- tional investigation of miRNAs. Particularly, the expres- sion data sets are manually annotated according to miRNA, target, tissue type, disease and perturbation, so that the user can easily focus on the subject of interest. The data set browser provides diverse access routes to our comprehensive miRNA-related data sets by miRNA, tissue type, etc. The data are hierarchically organized in Nucleic Acids Research, 2011, Vol. 39, Database issue D159 several tables with increasing details from top to bottom, e.g. from the full list of miRNAs to the actual expression values of each miRNA. The association analysis connects different miRNAs, diseases and perturbations by the overlap among miRNA/gene sets and by the similarity between miRNA expression/phenotype proﬁles. The asso- ciation analysis module is also equipped with an integrated association network viewer for convenient ex- ploration of association networks. Finally, the GSA/ miRSA module takes user-deﬁned gene sets or miRNA sets and performs GSA or miRSA against various types of gene annotations [e.g. gene ontology (GO, 13), KEGG (14)] as well as the miRGator data sets. DATA SOURCES AND PROCESSING The core data set of miRGator v2.0 consists of seven dif- ferent data types collected from various sources such as gene expression, miRNA-disease association and four major miRNA-target databases (TargetScan, PITA, miRanda and miBridge). The seven data types belong to one of the three broad categories$ miRNA set, gene set and miRNA proﬁles. Where appropriate, these data sets were Figure 1. System overview of miRGator v2.0. There are three main modules. The data set browser allows access to all the data sets by miRNA, tissue, disease and perturbation. Within the association analysis module, miRNAs, diseases and perturbations can be associated by GSA, miRSA and miRPA. The resulting association network is visualized by an integrated association network viewer. In the GSA/miRSA module, the user may enter a list of miRNAs/genes and perform GSA/miRSA against miRNA sets or gene sets in the miRGator system.