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Comparative Study
. 2010 Dec 2;11 Suppl 4(Suppl 4):S5.
doi: 10.1186/1471-2164-11-S4-S5.

dbDEMC: a database of differentially expressed miRNAs in human cancers

Zhen Yang  1 , Fei Ren, Changning Liu, Shunmin He, Gang Sun, Qian Gao, Lei Yao, Yangde Zhang, Ruoyu Miao, Ying Cao, Yi Zhao, Yang Zhong, Haitao Zhao
Affiliations
Comparative Study

dbDEMC: a database of differentially expressed miRNAs in human cancers

Zhen Yang et al. BMC Genomics. .

Abstract

Background: MicroRNAs (miRNAs) are small noncoding RNAs about 22 nt long that negatively regulate gene expression at the post-transcriptional level. Their key effects on various biological processes, e.g., embryonic development, cell division, differentiation and apoptosis, are widely recognized. Evidence suggests that aberrant expression of miRNAs may contribute to many types of human diseases, including cancer. Here we present a database of differentially expressed miRNAs in human cancers (dbDEMC), to explore aberrantly expressed miRNAs among different cancers.

Results: We collected the miRNA expression profiles of 14 cancer types, curated from 48 microarray data sets in peer-reviewed publications. The Significance Analysis of Microarrays method was used to retrieve the miRNAs that have dramatically different expression levels in cancers when compared to normal tissues. This database provides statistical results for differentially expressed miRNAs in each data set. A total of 607 differentially expressed miRNAs (590 mature miRNAs and 17 precursor miRNAs) were obtained in the current version of dbDEMC. Furthermore, low-throughput data from the same literature were also included in the database for validation. An easy-to-use web interface was designed for users. Annotations about each miRNA can be queried through miRNA ID or miRBase accession numbers, or can be browsed by different cancer types.

Conclusions: This database is expected to be a valuable source for identification of cancer-related miRNAs, thereby helping with the improvement of classification, diagnosis and treatment of human cancers. All the information is freely available through http://159.226.118.44/dbDEMC/index.html.

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Figures

Figure 1
Figure 1
The web interface of dbDEMC. (A) Key word search. miRNAs can be searched via miRNA ID or miRBase accession number. (B) Browse database, users can browse the miRNAs of specific cancers. (C) BLAST. An easy-to-use interface was created for parameter selection. (D) A part of search result page, consisting of a summary, an expression heatmap and the expression status.
Figure 2
Figure 2
Detailed page of an example miRNA record. The whole page consists of five major parts: a summary, an expression heatmap, statistical details, the D value across signatures, and the low-throughput data for validation.
Figure 3
Figure 3
Data content of dbDEMC. (A) The number of the differentially expressed miRNAs in each cancer type. (B) The number of the differentially expressed miRNAs in multiple cancers.
Figure 4
Figure 4
Meta-signature of multiple miRNAs. Seventy-four miRNAs have different expression level in at least 20 "cancer vs normal" signatures. Twenty cancer types were selected for this figure. Red boxes signify significant up-regulation in cancers compared to normal tissues, blue boxes signify significant down-regulation in cancers compared to normal tissues, and white boxes signify no significance or missing data.
See this image and copyright information in PMC

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