OMCD: OncomiR Cancer Database

Abstract

Background: microRNAs (miRNAs) are crucially important in the development of cancer. Their dysregulation, commonly observed in various types of cancer, is largely cancer-dependent. Thus, to understand the tumor biology and to develop accurate and sensitive biomarkers, we need to understand pan-cancer miRNA expression.

Constructions: At the University of Minnesota, we developed the OncomiR Cancer Database (OMCD), hosted on a web server, which allows easy and systematic comparative genomic analyses of miRNA sequencing data derived from more than 9500 cancer patients tissue samples available in the Cancer Genome Atlas (TCGA). OMCD includes associated clinical information and is searchable by organ-specific terms common to the TCGA.

Conclusions: Freely available to all users ( www.oncomir.umn.edu/omcd/ ), OMCD enables (1) simple visualization of TCGA miRNA sequencing data, (2) statistical analysis of differentially expressed miRNAs for each cancer type, and (3) exploration of miRNA clusters across cancer types. DATABASE URL: www.oncomir.umn.edu/omcd.

Keywords: Cancer; Database; OncomiR; TCGA; miRNA; miRNA expression profile; microRNA.

Fig. 1

Screenshots of our sample analyses of miR-21 in COAD. a, b Advanced Search options in OMCD, enabling searches by miRNA, by cancer types, and by statistical results. c Heatmap. d Numeric view of absolute expressions of miR-21 in COAD control and tumor samples. e Heat map of relative expression of miR-21 in COAD. f Information and external links. g Heat map of miR-21 cluster members, enabling exploration of the expression patterns of colocalized miRNAs. h Statistical results of group-based comparisons of miR-21 in different cancer types

Fig. 2

Heatmap of differentially expressed miRNAs in tumor vs. control samples (P < 0.000001, with a mean fold change in the tumor samples greater than 2 in 5 or more comparisons). Red = upregulation; green = downregulation