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This article is part of the supplement: Ninth International Conference on Bioinformatics (InCoB2010): Computational Biology

Open Access Proceedings

dbDEMC: a database of differentially expressed miRNAs in human cancers

Zhen Yang123, Fei Ren4, Changning Liu2, Shunmin He5, Gang Sun6, Qian Gao6, Lei Yao1, Yangde Zhang4, Ruoyu Miao3, Ying Cao78, Yi Zhao2*, Yang Zhong19* and Haitao Zhao3*

Author Affiliations

1 School of Life Science, Fudan University, Shanghai, 200433, China

2 Bioinformatics Research Group, Center for Advanced Computing Technology Research, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100080, China

3 Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, CAMS & PUMC, Beijing, 100730, China

4 Central South University, Changsha, 410083, China

5 Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China

6 Key Laboratory of Medical Molecular Virology, Institutes of Biomedical Sciences and Institute of Medical Microbiology, Fudan University, Shanghai, 200032, China

7 The Institute of Statistical Mathematics, 10-3 Midori-cho, Tachikawa, Tokyo, 190-8562, Japan

8 Department of Biosystems Science, The Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan

9 Shanghai Center for Bioinformation Technology, Shanghai, 200235, China

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BMC Genomics 2010, 11(Suppl 4):S5  doi:10.1186/1471-2164-11-S4-S5

Published: 2 December 2010

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 webcite.