D160 Nucleic Acids Research, 2011, Vol. 39, Database issue Figure 2. The overall procedure of data collection and processing. manually curated according to tissue, disease and perturb- ation (e.g. chemical treatment). The overall procedure of data collection and processing is shown in Figure 2. The miRNA set category is basically a list of miRNAs. This category consists of known disease-miRNA associ- ations from PhenomiR (8) and differentially expressed miRNAs (DEmiRs) from the gene expression omnibus (GEO) (15) and ArrayExpress (16). For DEmiRs, we col- lected miRNA expression data for various cancers and perturbations. In total, 154 miRNA expression data sets (8431 proﬁles) were downloaded from the GEO and ArrayExpress. The miRNA expression proﬁles were quantile normalized using LIMMA package (17). The miRNA proﬁles were hand-curated, resulting in the anno- tations of 26 human tissue types, 56 diseases and 83 perturbations. The gene set category contains information for miRNA targets such as predicted miRNA targets, anti-coexpressed miRNA-gene pairs and miRNA-perturbed differentially expressed genes (DEGs) (i.e. the up-regulated genes under miRNA-knockout conditions and down-regulated genes under miRNA-overexpression conditions). The pre- dicted miRNA targets were collected from TargetScan, PITA, miRanda and miBridge. The miRNA-perturbed gene expression proﬁles were obtained from GEO. We compiled 68 data sets of 613 gene expression proﬁles, where one or more miRNAs were knocked out/down or overexpressed. After ﬁltering out inappropriate sets, the remaining 63 sets contain 595 proﬁles annotated with 88 miRNA perturbations (90 different miRNAs), 15 tissues and 18 diseases. For anti-coexpressed gene sets, we col- lected 22 data sets from GEO, where both miRNA and mRNA expression proﬁles were measured for the same sample. The total number of the paired miRNA and mRNA proﬁles was 1265 and 1568, respectively. Pearson correlation between miRNA and mRNA expression values was calculated for each of the 22 data sets. Accordingly, a miRNA–mRNA pair may have up to 22 correlation values. We compiled anti-coexpressed miRNA–mRNA pairs, which show signiﬁcant anti-correlation in at least two or more cases among the 22 data sets at P-value cut off <0.001. For miRNAs with more than 500 anti-correlated mRNAs above cut-off, we took only the top 500 mRNAs ranked by the sum of –log (P-value). The last category is miRNA-related proﬁle, which consists of miRNA expression proﬁles and phenotypic proﬁles. The miRNA expression proﬁles came from the same data used in the DEmiR set. Phenotypic proﬁles were obtained from the PhenomiR data describing up/ down regulation of miRNAs in various diseases. Additionally, various types of gene annotation informa- tion are integrated including GO and biological pathways (KEGG, BioCarta). The details of data source, type and statistics are shown in Table 1 and on-line. DATA SET BROWSER From the data set browser, the user can access all the data sets complied in miRGator v2.0, which are organized ac- cording to miRNA, target, tissue type, disease and per- turbation. Accordingly, the user may access the data set of interest using various annotation categories of choice. Several tables are sequentially displayed from top to bottom with increasing detail as the user chooses an item of interest. For example, the user can start from