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LncRNADisease


NAR Molecular Biology Database Collection entry number 1579
Geng Chen1,2,3#, Ziyun Wang2#, Dongqing Wang2#, Chengxiang Qiu2, Mingxi Liu4, Xing Chen4, Qipeng Zhang2, Guiying Yan4*, and Qinghua Cui1,2,3*
1 Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, 38 Xueyuan Rd, Beijing, 100191, China 2 MOE Key Lab of Cardiovascular Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China 3 Institute of Systems Biomedicine, Peking University, 38 Xueyuan Road, Beijing, 100191, China 4 Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China.

Database Description

A surprising finding in human transcriptome analysis is that protein-coding sequences only account for a small portion of the genome transcripts (1). The majority of the human genome transcripts are noncoding RNAs, in particular, long noncoding RNAs (lncRNAs) (2). In recent years, accumulating studies have revealed that a number of lncRNAs are not transcriptional noise but have important functions. More recently, researchers have attempted to understand the relationships between lncRNAs and diseases. Studies have reported that lncRNA dysfunctions are associated with a broad range of diseases (3), including cancers (4), cardiovascular diseases(5), and neurodegeneration diseases (6).
The study of lncRNA-disease associations is becoming one of the most important topics of lncRNAs and diseases. For this reason, a high quality lncRNA-disease association database will be helpful in studying the roles of lncRNAs in diseases but is still not available. In this paper, we describe a long noncoding RNA (lncRNA) and disease association database (LncRNADisease), which is publicly accessible at http://cmbi.bjmu.edu.cn/lncrnadisease.
LncRNADisease database collected and curated ~480 entries of experimentally supported lncRNA-disease associations including 166 diseases. LncRNADisease also curated 478 entries of lncRNA interacting partners at various molecular levels, including protein, RNA, miRNA, and DNA.Moreover, we annotated lncRNA-disease associations with genomic information, sequences, references, and species. We normalized the disease name and the type of lncRNA dysfunction and provided a detailed description for each entry. Finally, we developed a bioinformatic method to predict novel lncRNA-disease associations and integrated the method and the predicted associated diseases of 1, 564 human lncRNAs into the database.

Acknowledgements

We thank National Basic Research program of China (2012CB517500) and National Natural Science Foundation of China (Nos. 31000585 and 11021161) for supporting this project.

References

1. Bertone, P., Stolc, V., Royce, T.E., Rozowsky, J.S., Urban, A.E., Zhu, X., Rinn, J.L., Tongprasit, W., Samanta, M., Weissman, S. et al. (2004) Global identification of human transcribed sequences with genome tiling arrays. Science, 306, 2242-2246.

2. Kapranov, P., Cheng, J., Dike, S., Nix, D.A., Duttagupta, R., Willingham, A.T., Stadler, P.F., Hertel, J., Hackermuller, J., Hofacker, I.L. et al. (2007) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science, 316,1484-1488.

3. Ponting, C.P., Oliver, P.L. and Reik, W. (2009) Evolution and functions of long noncoding RNAs. Cell, 136, 629-641.

4. Spizzo, R., Almeida, M.I., Colombatti, A. and Calin, G.A. (2012) Long non-coding RNAs and cancer: a new frontier of translatonal research? Oncogene.

5. Congrains, A., Kamide, K., Oguro, R., Yasuda, O., Miyata, K., Yamamoto, E., Kawai, T., Kusunoki, H., Yamamoto, H., Takeya, Y. et al. (2012) Genetic variants at the 9p21 locus contribute to atherosclerosis through modulation of ANRIL and CDKN2A/B. Atherosclerosis, 220, 449-455.

6. Johnson, R. (2012) Long non-coding RNAs in Huntington's disease neurodegeneration. Neurobiol Dis, 46, 245-254.



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