PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes

Abstract

In recent years, microRNAs have been shown to play important roles in physiological as well as malignant processes. The PhenomiR database http://mips.helmholtz-muenchen.de/phenomir provides data from 542 studies that investigate deregulation of microRNA expression in diseases and biological processes as a systematic, manually curated resource. Using the PhenomiR dataset, we could demonstrate that, depending on disease type, independent information from cell culture studies contrasts with conclusions drawn from patient studies.

Figure 1

Overview of the PhenomiR web page, the search options, search results and a database entry.

Figure 2

Overview of a PhenomiR entry structure.

Figure 3

Fraction of annotated miRNA detection methods and diseases in PhenomiR. (a) Distribution of detection methods for all disease entries in PhenomiR. (b) Distribution of disease entries in PhenomiR.

Figure 4

Comparison of consistencies in expression profiles between in vivo and in vitro experiments.

Figure 5

miRNA cluster enrichment in human diseases. For each disease the log-odds (LOD) score is plotted. There is an enrichment of miRNA cluster members for 46 diseases (88.5%). miRNA cluster members are, on average, 1.4 times (LOD = 0.58) enriched compared to random. Green points depict enriched diseases (at least LOD = 0.15 for lung cancer). Black points indicate diseases without enrichment compared to random and red points depict disorders with few deregulated cluster members. For abbreviations of disease names see Additional file 13.