LincSNP 2.0: An updated database for linking disease-associated SNPs to human long non-coding RNAs and their TFBSs

Nucleic Acids Research

Volumn 45, Issue D1, 2017, Pages D74-D78

  Ning, Shangwei ^a   Yue, Ming ^a   Wang, Peng ^a   Liu, Yue ^a   Zhi, Hui ^a   Zhang, Yan ^a   Zhang, Jizhou ^a   Gao, Yue ^a   Guo, Maoni ^a   Zhou, Dianshuang ^a   Li, Xia ^a   Li, Xin ^a  

^a HARBIN MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

LONG UNTRANSLATED RNA; TRANSCRIPTION FACTOR;

ARTICLE; BINDING SITE; DATA BASE; DISEASE ASSOCIATION; GENETIC LINKAGE; GENOME-WIDE ASSOCIATION STUDY; HIGH THROUGHPUT SEQUENCING; HUMAN; PRIORITY JOURNAL; RNA SEQUENCE; SCORING SYSTEM; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTION FACTOR BINDING SITE; DISEASES; GENETIC DATABASE; GENETICS; METABOLISM; MOLECULAR GENETICS; REGULATORY SEQUENCE; SOFTWARE;

BINDING SITES; DATABASES, GENETIC; DISEASE; HUMANS; MOLECULAR SEQUENCE ANNOTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; REGULATORY ELEMENTS, TRANSCRIPTIONAL; RNA, LONG NONCODING; SOFTWARE; TRANSCRIPTION FACTORS;

EID: 85023613680     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw945     Document Type: Article

References (36)

1. Ponting, C.R., Oliver, P.L. and Reik, W. (2009) Evolution and functions of long noncoding RNAs. Cell, 136, 629-641.
2. Rinn, J.L. and Chang, H.Y. (2012) Genome regulation by long noncoding RNAs. Annu. Rev. Biochem., 81, 145-166.
3. Geisler, S. and Coller, J. (2013) RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts. Nat. Rev. Mol. Cell Biol, 14, 699-712.
4. Fatica, A. and Bozzoni, I. (2014) Long non-coding RNAs: new players in cell differentiation and development. Nat. Rev. Genet., 15, 7-21.
5. Huarte, M. (2015) The emerging role of IncRNAs in cancer. Nat. Med, 21, 1253-1261.
6. Esteller, M. (2011) Non-coding RNAs in human disease. Nat. Rev Genet., 12, 861-874.
7. Jin, G., Sun, J., Isaacs, S.D., Wiley, K.E., Kim, S.T., Chu, L.W., Zhang, Z., Zhao, H., Zheng, S.L., Isaacs, W.B. et al. (2011) Human polymorphisms at long non-coding RNAs (lncRNAs) and association with prostate cancer risk. Carcinogenesis, 32, 1655-1659.
8. Li, D., Song, L., Wen, Z., Li, X., Jie, J., Wang, Y. and Peng, L. (2016) Strong evidence for IncRNA ZNRD1-AS1, and its functional Cis-eQTL locus contributing more to the susceptibility of lung cancer. Oncotarget, 7, 35813-35817.
9. Ning, S., Zhao, Z., Ye, J., Wang, P., Zhi, H., Li, R., Wang, T. and Li, X. (2014) LincSNP: a database of linking disease-associated SNPs to human large intergenic non-coding RNAs. BMC Bioinformatics, 15, 152.
10. Jendrzejewski, J., He, H., Radomska, H.S., Li, W., Tomsic, J., Liyanarachchi, S., Davuluri, R.V, Nagy, R. and de la Chapelle, A. (2012) The polymorphism rs944289 predisposes to papillary thyroid carcinoma through a large intergenic noncoding RNA gene of tumor suppressor type. Proc. Natl. Acad. Sci. U.S.A., 109, 8646-8651.
11. Xie, C, Yuan, J., Li, H., Li, M., Zhao, G., Bu, D., Zhu, W., Wu, W., Chen, R. and Zhao, Y. (2014) NONCODEv4: exploring the world of long non-coding RNA genes. Nucleic Acids Res., 42, D98-D103.
12. Paraskevopoulou, M.D., Georgakilas, G., Kostoulas, N, Reczko, M., Maragkakis, M., Dalamagas, T.M. and Hatzigeorgiou, A.G. (2013) DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs. Nucleic Acids Res., 41, D239-D245.
13. Volders, PJ, Verheggen, K., Menschaert, G, Vandepoele, K., Martens, L., Vandesompele, J. and Mestdagh, P (2015) An update on LNCipedia: a database for annotated human IncRNA sequences. Nucleic Acids Res., 43, D174-D180.
14. Quek, X.C., Thomson, D.W., Maag, J.L., Bartonicek, N, Signal, B., Clark, M.B., Gloss, B.S. and Dinger, M.E. (2015) IncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs. Nucleic Acids Res., 43, D168-D173.
15. Ma, L., Li, A., Zou, D., Xu, X., Xia, L., Yu, J., Bajic, VB. and Zhang, Z. (2015) IncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs. Nucleic Acids Res., 43, D187-D192.
16. Yang, J.H., Li, J.H., Jiang, S., Zhou, H. and Qu, L.H. (2013) ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. Nucleic Acids Res., 41, D177-D187.
17. Li, J.H., Liu, S., Zhou, H., Qu, L.H. and 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.
18. Chen, G, Wang, Z., Wang, D., Qiu, C, Liu, M., Chen, X., Zhang, Q., Yan, G and Cui, Q. (2013) IncRNADisease: a database for long-non-coding RNA-associated diseases. Nucleic Acids Res, 41, D983-D986.
19. Ning, S., Zhang, J., Wang, P, Zhi, H., Wang, J., Liu, Y, Gao, Y, Guo, M., Yue, M., Wang, L. et al. (2016) Inc2Cancer: a manually curated database of experimentally supported IncRNAs associated with various human cancers. Nucleic Acids Res., 44, D980-D985.
20. Gong, J., Liu, W., Zhang, J., Miao, X. and Guo, AY. (2015) IncRNASNP: a database of SNPs in IncRNAs and their potential functions in human and mouse. Nucleic Acids Res., 43, D181-D186.
21. 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.
22. Li, M.J., Liu, Z., Wang, P, Wong, M.P, Nelson, M.R., Kocher, J.P, Yeager, M., Sham, PC, Chanock, S.J., Xia, Z. et al. (2016) GWASdb v2: an update database for human genetic variants identified by genome-wide association studies. Nucleic Acids Res., 44, D869-D876.
23. Mailman, M.D., Feolo, M., Jin, Y, Kimura, M., Tryka, K., Bagoutdinov, R., Hao, L., Kiang, A., Paschall, J., Phan, L. et al. (2007) The NCBI dbGaP database of genotypes and phenotypes. Nat. Genet., 39, 1181-1186.
24. Becker, K.G., Barnes, K.C, Bright, TJ. and Wang, S.A. (2004) The genetic association database. Nat. Genet., 36, 431-432.
25. Beck, T, Hastings, R.K., Gollapudi, S., Free, R.C. and Brookes, A.J. (2014) GWAS Central: a comprehensive resource for the comparison and interrogation of genome-wide association studies. Eur. J. Hum. Genet., 22, 949-952.
26. Johnson, A.D. and O'Donnell, C.J. (2009) An open access database of genome-wide association results. BMC Med. Genet., 10, 6.
27. Welter, D., MacArthur, J., Morales, J., Burdett, T, Hall, P, Junkins, H., Klemm, A., Flicek, P, Manolio, T, Hindorff, L. et al. (2014) The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res., 42, D1001-D1006.
28. Altman, R.B. (2007) PharmGKB: a logical home for knowledge relating genotype to drug response phenotype. Nat. Genet., 39, 426.
29. Eicher, J.D., Landowski, C, Stackhouse, B., Sloan, A., Chen, W., Jensen, N, Lien, J.P, Leslie, R. and Johnson, A.D. (2015) GRASP v2.0: an update on the Genome-Wide Repository of Associations between SNPs and phenotypes. Nucleic Acids Res, 43, D799-D804.
30. Danecek, P, Auton, A., Abecasis, G, Albers, C.A., Banks, E., DePristo, M.A., Handsaker, R.E., Lunter, G, Marth, GT, Sherry, S.T et al. (2011) The variant call format and VCFtools. Bioinformatics, 27, 2156-2158.
31. Ning, S., Zhao, Z., Ye, J., Wang, P, Zhi, H., Li, R., Wang, T, Wang, J., Wang, L. and Li, X. (2014) SNP@lincTFBS: an integrated database of polymorphisms in human LincRNA transcription factor binding sites. PLoS One, 9, e103851.
32. Rosenbloom, K.R., Armstrong, J., Barber, GP, Casper, J., Clawson, H., Diekhans, M., Dreszer, TR, Fujita, PA., Guruvadoo, L., Haeussler, M. et al. (2015) The UCSC Genome Browser database: 2015 update. Nucleic Acids Res., 43, D670-D681.
33. Hsu, S.D., Tseng, YT, Shrestha, S., Lin Y.L., Khaleel, A., Chou, CH., Chu, CF, Huang, HY, Lin, CM., Ho, SY. et al. (2014)miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic Acids Res., 42, D78-D85.
34. Jiang, Q., Wang Y., Hao, Y, Juan, L., Teng, M., Zhang, X., Li, M., Wang, G and Liu, Y (2009) miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res., 37, D98-D104.
35. Li, Y, Qiu, C, Tu, J., Geng, B., Yang, J., Jiang, T and Cui, Q. (2014) HMDD v2.0: a database for experimentally supported human microRNA and disease associations. Nucleic Acids Res., 42, D1070-D1074.
36. Coordinators, NR. (2015) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 43, D6-D17.