LncDisease: A sequence based bioinformatics tool for predicting lncRNA-disease associations

Nucleic Acids Research

Volumn 44, Issue 9, 2016, Pages

  Wang, Junyi ^a,b   Ma, Ruixia ^c   Ma, Wei ^a,b   Chen, Ji ^a,b   Yang, Jichun ^a,b   Xi, Yaguang ^c   Cui, Qinghua ^a,b,d  

^a PEKING UNIVERSITY HEALTH SCIENCE CENTER   (China)

^b BEIJING UNIVERSITY OF POSTS AND TELECOMMUNICATIONS   (China)

^c UNIVERSITY OF SOUTH ALABAMA   (United States)

^d PEKING UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ANGIOTENSIN II; LONG UNTRANSLATED RNA; MICRORNA;

ARTICLE; BIOINFORMATICS; BREAST CANCER; BREAST CANCER CELL LINE; CELL STIMULATION; COMPUTER PROGRAM; CONTROLLED STUDY; DATA MINING; GENETIC ASSOCIATION; GENETIC DISORDER; HUMAN; HUMAN CELL; HYPERTENSION; MCF 7 CELL LINE; MDA MB 231 CELL LINE; PREDICTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; RNA SEQUENCE; VALIDATION STUDY; VASCULAR SMOOTH MUSCLE CELL; BIOLOGY; BREAST TUMOR; CYTOLOGY; DRUG EFFECTS; FEMALE; GENETICS; MCF-7 CELL LINE; PROCEDURES; SOFTWARE; TUMOR CELL LINE; VASCULAR SMOOTH MUSCLE;

ANGIOTENSIN II; BREAST NEOPLASMS; CELL LINE, TUMOR; COMPUTATIONAL BIOLOGY; FEMALE; HUMANS; HYPERTENSION; MCF-7 CELLS; MICRORNAS; MUSCLE, SMOOTH, VASCULAR; RNA, LONG NONCODING; SOFTWARE;

EID: 84969921106     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw093     Document Type: Article

References (44)

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., Reik, W. (2009) Evolution and functions of long noncoding RNAs. Cell, 136, 629-641.
4. Chu, C., Spitale, R.C., Chang, H.Y. (2015) Technologies to probe functions and mechanisms of long noncoding RNAs. Nat. Struct. Mol. Biol., 22, 29-35.
5. Kataoka, M., Wang, D.Z. (2014) Non-coding RNAs including miRNAs and lncRNAs in cardiovascular biology and disease. Cells, 3, 883-898.
6. Chakravarty, D., Sboner, A., Nair, S.S., Giannopoulou, E., Li, R., Hennig, S., Mosquera, J.M., Pauwels, J., Park, K., Kossai, M. et al. (2014) The oestrogen receptor alpha-regulated lncRNA NEAT1 is a critical modulator of prostate cancer. Nat. Commun., 5, 5383.
7. Chen, G., Wang, Z., Wang, D., Qiu, C., Liu, M., Chen, X., Zhang, Q., Yan, G., Cui, Q. (2013) LncRNADisease: a database for long-non-coding RNA-associated diseases. Nucleic Acids Res., 41, D983-D986.
8. Wapinski, O., Chang, H.Y. (2011) Long noncoding RNAs and human disease. Trends Cell Biol., 21, 354-361.
9. Bu, D., Yu, K., Sun, S., Xie, C., Skogerbo, G., Miao, R., Xiao, H., Liao, Q., Luo, H., Zhao, G. et al. (2012) NONCODE v3.0: integrative annotation of long noncoding RNAs. Nucleic Acids Res., 40, D210-D215.
10. Iyer, M.K., Niknafs, Y.S., Malik, R., Singhal, U., Sahu, A., Hosono, Y., Barrette, T.R., Prensner, J.R., Evans, J.R., Zhao, S. et al. (2015) The landscape of long noncoding RNAs in the human transcriptome. Nat. Genet., 47, 199-208.
11. Li, J., Gao, C., Wang, Y., Ma, W., Tu, J., Wang, J., Chen, Z., Kong, W., Cui, Q. (2014) A bioinformatics method for predicting long noncoding RNAs associated with vascular disease. Sci. China. Life Sci., 57, 852-857.
12. Sun, L., Luo, H., Liao, Q., Bu, D., Zhao, G., Liu, C., Liu, Y., Zhao, Y. (2013) Systematic study of human long intergenic non-coding RNAs and their impact on cancer. Sci. China. Life Sci., 56, 324-334.
13. Liu, M.X., Chen, X., Chen, G., Cui, Q.H., Yan, G.Y. (2014) A computational framework to infer human disease-associated long noncoding RNAs. PloS One, 9, e84408.
14. Hao, Y., Wu, W., Shi, F., Dalmolin, R.J., Yan, M., Tian, F., Chen, X., Chen, G., Cao, W. (2015) Prediction of long noncoding RNA functions with co-expression network in esophageal squamous cell carcinoma. BMC Cancer, 15, 168.
15. Chen, X., Yan, G.Y. (2013) Novel human lncRNA-disease association inference based on lncRNA expression profiles. Bioinformatics, 29, 2617-2624.
16. Bialkowska-Hobrzanska, H., Driman, D.K., Fletcher, R., Harry, V., Razvi, H. (2006) Expression of human telomerase reverse transcriptase, Survivin, DD3 and PCGEM1 messenger RNA in archival prostate carcinoma tissue. Can. J. Urol., 13, 2967-2974.
17. Ganegoda, G.U., Li, M., Wang, W., Feng, Q. (2015) Heterogeneous network model to infer human disease-long intergenic non-coding RNA associations. IEEE Trans. Nanobioscience, 14, 175-183.
18. Sun, J., Shi, H., Wang, Z., Zhang, C., Liu, L., Wang, L., He, W., Hao, D., Liu, S., Zhou, M. (2014) Inferring novel lncRNA-disease associations based on a random walk model of a lncRNA functional similarity network. Mol. BioSyst., 10, 2074-2081.
19. Yang, X., Gao, L., Guo, X., Shi, X., Wu, H., Song, F., Wang, B. (2014) A network based method for analysis of lncRNA-disease associations and prediction of lncRNAs implicated in diseases. PloS One, 9, e87797.
20. Zhou, M., Wang, X., Li, J., Hao, D., Wang, Z., Shi, H., Han, L., Zhou, H., Sun, J. (2015) Prioritizing candidate disease-related long non-coding RNAs by walking on the heterogeneous lncRNA and disease network. Mol. BioSyst., 11, 760-769.
21. Li, J.H., Liu, S., Zhou, H., Qu, L.H., Yang, J.H. (2014) starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res., 42, D92-D97.
22. Paraskevopoulou, M.D., Georgakilas, G., Kostoulas, N., Reczko, M., Maragkakis, M., Dalamagas, T.M., Hatzigeorgiou, A.G. (2013) DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs. Nucleic Acids Res., 41, D239-D245.
23. Li, Y., Qiu, C., Tu, J., Geng, B., Yang, J., Jiang, T., Cui, Q. (2014) HMDD v2.0: a database for experimentally supported human microRNA and disease associations. Nucleic Acids Res., 42, D1070-D1074.
24. Lu, M., Zhang, Q., Deng, M., Miao, J., Guo, Y., Gao, W., Cui, Q. (2008) An analysis of human microRNA and disease associations. PloS One, 3, e3420.
25. Lu, M., Shi, B., Wang, J., Cao, Q., Cui, Q. (2010) TAM: a method for enrichment and depletion analysis of a microRNA category in a list of microRNAs. BMC Bioinformatics, 11, 419.
26. Qiu, C., Chen, G., Cui, Q. (2012) Towards the understanding of microRNA and environmental factor interactions and their relationships to human diseases. Sci. Rep., 2, 318.
27. Chen, X. (2015) Predicting lncRNA-disease associations and constructing lncRNA functional similarity network based on the information of miRNA. Sci. Rep., 5, 13186.
28. Volders, P.J., Helsens, K., Wang, X., Menten, B., Martens, L., Gevaert, K., Vandesompele, J., Mestdagh, P. (2013) LNCipedia: a database for annotated human lncRNA transcript sequences and structures. Nucleic Acids Res., 41, D246-D251.
29. Poliseno, L., Salmena, L., Zhang, J., Carver, B., Haveman, W.J., Pandolfi, P.P. (2010) A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature, 465, 1033-1038.
30. Bartel, D.P. (2009) MicroRNAs: target recognition and regulatory functions. Cell, 136, 215-233.
31. Friedman, R.C., Farh, K.K., Burge, C.B., Bartel, D.P. (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res., 19, 92-105.
32. Betel, D., Wilson, M., Gabow, A., Marks, D.S., Sander, C. (2008) The microRNA.org resource: targets and expression. Nucleic Acids Res., 36, D149-D153.
33. Wang, C., Chen, Z., Li, S., Zhang, Y., Jia, S., Li, J., Chi, Y., Miao, Y., Guan, Y., Yang, J. (2014) Hepatic overexpression of ATP synthase beta subunit activates PI3K/Akt pathway to ameliorate hyperglycemia of diabetic mice. Diabetes, 63, 947-959.
34. Wang, C., Chi, Y., Li, J., Miao, Y., Li, S., Su, W., Jia, S., Chen, Z., Du, S., Zhang, X. et al. (2014) FAM3A activates PI3K p110alpha/Akt signaling to ameliorate hepatic gluconeogenesis and lipogenesis. Hepatology, 59, 1779-1790.
35. Prasad, A.M., Morgan, D.A., Nuno, D.W., Ketsawatsomkron, P., Bair, T.B., Venema, A.N., Dibbern, M.E., Kutschke, W.J., Weiss, R.M., Lamping, K.G. et al. (2015) Calcium/calmodulin-dependent kinase II inhibition in smooth muscle reduces angiotensin II-induced hypertension by controlling aortic remodeling and baroreceptor function. J Am. Heart Assoc., 4, e001949.
36. Chang, L., Li, C., Lan, T., Wu, L., Yuan, Y., Liu, Q., Liu, Z. (2015) Decreased expression of long non-coding RNA GAS5 indicates a poor prognosis and promotes cell proliferation and invasion in hepatocellular carcinoma by regulating vimentin. Mol. Med. Rep., 13, 1541-1550.
37. Hu, L., Ye, H., Huang, G., Luo, F., Liu, Y., Liu, Y., Yang, X., Shen, J., Liu, Q., Zhang, J. (2015) Long noncoding RNA GAS5 suppresses the migration and invasion of hepatocellular carcinoma cells via miR-21. Tumour Biol., doi:10.1007/s13277-015-4111-x.
38. Tao, R., Hu, S., Wang, S., Zhou, X., Zhang, Q., Wang, C., Zhao, X., Zhou, W., Zhang, S., Li, C. et al. (2015) Association between indel polymorphism in the promoter region of lncRNA GAS5 and the risk of hepatocellular carcinoma. Carcinogenesis, 36, 1136-1143.
39. Tu, Z.Q., Li, R.J., Mei, J.Z., Li, X.H. (2014) Down-regulation of long non-coding RNA GAS5 is associated with the prognosis of hepatocellular carcinoma. Int. J. Clin. Exp. Pathol., 7, 4303-4309.
40. Yu, F., Zheng, J., Mao, Y., Dong, P., Lu, Z., Li, G., Guo, C., Liu, Z., Fan, X. (2015) Long non-coding RNA growth arrest-specific transcript 5 (GAS5) inhibits liver fibrogenesis through a mechanism of competing endogenous RNA. J. Biol. Chem., 290, 28286-28298.
41. Qiao, H.P., Gao, W.S., Huo, J.X., Yang, Z.S. (2013) Long non-coding RNA GAS5 functions as a tumor suppressor in renal cell carcinoma. Asian Pac. J. Cancer Prev., 14, 1077-1082.
42. Zhou, S., Wang, J., Zhang, Z. (2014) An emerging understanding of long noncoding RNAs in kidney cancer. J. Cancer Res. Clin. Oncol., 140, 1989-1995.
43. Dong, S., Qu, X., Li, W., Zhong, X., Li, P., Yang, S., Chen, X., Shao, M., Zhang, L. (2015) The long non-coding RNA, GAS5, enhances gefitinib-induced cell death in innate EGFR tyrosine kinase inhibitor-resistant lung adenocarcinoma cells with wide-type EGFR via downregulation of the IGF-1R expression. J. Hematol. Oncol., 8, 43.
44. Zhou, Y., Wu, K., Jiang, J., Huang, J., Zhang, P., Zhu, Y., Hu, G., Lang, J., Shi, Y., Hu, L. et al. (2015) Integrative analysis reveals enhanced regulatory effects of human long intergenic non-coding RNAs in lung adenocarcinoma. J. Genet. Genomics, 42, 423-436.