LincSNP: a database of linking disease-associated SNPs to human large intergenic non-coding RNAs

BMC Bioinformatics

Shangwei Ning¹  Zuxianglan Zhao¹  Jingrun Ye¹  Peng Wang¹  Hui Zhi¹  Ronghong Li¹  Tingting Wang¹  Xia Li¹ 

[1] College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China

关键词: Database;    Non-coding RNA;    GWAS;    Disease-associated SNPs;    LincRNA;   

Others  :  1087572
DOI  :  10.1186/1471-2105-15-152

 received in 2014-01-20, accepted in 2014-05-14,  发布年份 2014

【 摘 要 】

Background

Genome-wide association studies (GWAS) have successfully identified a large number of single nucleotide polymorphisms (SNPs) that are associated with a wide range of human diseases. However, many of these disease-associated SNPs are located in non-coding regions and have remained largely unexplained. Recent findings indicate that disease-associated SNPs in human large intergenic non-coding RNA (lincRNA) may lead to susceptibility to diseases through their effects on lincRNA expression. There is, therefore, a need to specifically record these SNPs and annotate them as potential candidates for disease.

Description

We have built LincSNP, an integrated database, to identify and annotate disease-associated SNPs in human lincRNAs. The current release of LincSNP contains approximately 140,000 disease-associated SNPs (or linkage disequilibrium SNPs), which can be mapped to around 5,000 human lincRNAs, together with their comprehensive functional annotations. The database also contains annotated, experimentally supported SNP-lincRNA-disease associations and disease-associated lincRNAs. It provides flexible search options for data extraction and searches can be performed by disease/phenotype name, SNP ID, lincRNA name and chromosome region. In addition, we provide users with a link to download all the data from LincSNP and have developed a web interface for the submission of novel identified SNP-lincRNA-disease associations.

Conclusions

The LincSNP database aims to integrate disease-associated SNPs and human lincRNAs, which will be an important resource for the investigation of the functions and mechanisms of lincRNAs in human disease. The database is available at http://bioinfo.hrbmu.edu.cn/LincSNP webcite.

【 授权许可】

   
2014 Ning et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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【 参考文献 】

• [1]Freimer NB, Sabatti C: Human genetics: variants in common diseases. Nature 2007, 445(7130):828-830.
• [2]Ward LD, Kellis M: Interpreting noncoding genetic variation in complex traits and human disease. Nat Biotechnol 2012, 30(11):1095-1106.
• [3]Pasmant E, Sabbagh A, Vidaud M, Bieche I: ANRIL, a long, noncoding RNA, is an unexpected major hotspot in GWAS. Faseb J 2010, 25(2):444-448.
• [4]Ponting CP, Oliver PL, Reik W: Evolution and functions of long noncoding RNAs. Cell 2009, 136(4):629-641.
• [5]Wilusz JE, Sunwoo H, Spector DL: Long noncoding RNAs: functional surprises from the RNA world. Genes Dev 2009, 23(13):1494-1504.
• [6]Tsai MC, Spitale RC, Chang HY: Long intergenic noncoding RNAs: new links in cancer progression. Cancer Res 2011, 71(1):3-7.
• [7]Wapinski O, Chang HY: Long noncoding RNAs and human disease. Trends Cell Biol 2011, 21(6):354-361.
• [8]Sethupathy P, Collins FS: MicroRNA target site polymorphisms and human disease. Trends Genet 2008, 24(10):489-497.
• [9]Ryan BM, Robles AI, Harris CC: Genetic variation in microRNA networks: the implications for cancer research. Nat Rev Cancer 2010, 10(6):389-402.
• [10]Bartel DP: MicroRNAs: target recognition and regulatory functions. Cell 2009, 136(2):215-233.
• [11]Hu Z, Bruno AE: The influence of 3’UTRs on MicroRNA function inferred from human SNP data. Comp Funct Genom 2011, 2011:910769.
• [12]Saunders MA, Liang H, Li WH: Human polymorphism at microRNAs and microRNA target sites. Proc Natl Acad Sci U S A 2007, 104(9):3300-3305.
• [13]Jendrzejewski J, He H, Radomska HS, Li W, Tomsic J, Liyanarachchi S, Davuluri RV, Nagy R, de la Chapelle A: 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 2012, 109(22):8646-8651.
• [14]Jin G, Sun J, Isaacs SD, Wiley KE, Kim ST, Chu LW, Zhang Z, Zhao H, Zheng SL, Isaacs WB, Xu J: Human polymorphisms at long non-coding RNAs (lncRNAs) and association with prostate cancer risk. Carcinogenesis 2011, 32(11):1655-1659.
• [15]Liu Y, Pan S, Liu L, Zhai X, Liu J, Wen J, Zhang Y, Chen J, Shen H, Hu Z: A genetic variant in long non-coding RNA HULC contributes to risk of HBV-related hepatocellular carcinoma in a Chinese population. PLoS One 2012, 7(4):e35145.
• [16]Kumar V, Westra HJ, Karjalainen J, Zhernakova DV, Esko T, Hrdlickova B, Almeida R, Zhernakova A, Reinmaa E, Vosa U, Hofker MH, Fehrmann RS, Fu J, Withoff S, Metspalu A, Franke L, Wijmenga C: Human disease-associated genetic variation impacts large intergenic non-coding RNA expression. PLoS Genet 2013, 9(1):e1003201.
• [17]Cunnington MS, Santibanez Koref M, Mayosi BM, Burn J, Keavney B: Chromosome 9p21 SNPs associated with multiple disease phenotypes correlate with ANRIL expression. PLoS Genet 2010, 6(4):e1000899.
• [18]Mailman MD, Feolo M, Jin Y, Kimura M, Tryka K, Bagoutdinov R, Hao L, Kiang A, Paschall J, Phan L, Popova N, Pretel S, Ziyabari L, Lee M, Shao Y, Wang ZY, Sirotkin K, Ward M, Kholodov M, Zbicz K, Beck J, Kimelman M, Shevelev S, Preuss D, Yaschenko E, Graeff A, Ostell J, Sherry ST: The NCBI dbGaP database of genotypes and phenotypes. Nat Genet 2007, 39(10):1181-1186.
• [19]Becker KG, Barnes KC, Bright TJ, Wang SA: The genetic association database. Nat Genet 2004, 36(5):431-432.
• [20]Thorisson GA, Lancaster O, Free RC, Hastings RK, Sarmah P, Dash D, Brahmachari SK, Brookes AJ: HGVbaseG2P: a central genetic association database. Nucleic Acids Res 2009, 37(Database issue):D797-D802.
• [21]Johnson AD, O’Donnell CJ: An open access database of genome-wide association results. BMC Med Genet 2009, 10:6.
• [22]Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA: Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A 2009, 106(23):9362-9367.
• [23]Altman RB: PharmGKB: a logical home for knowledge relating genotype to drug response phenotype. Nat Genet 2007, 39(4):426.
• [24]C WTCC: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 2007, 447(7145):661-678.
• [25]Begum F, Ghosh D, Tseng GC, Feingold E: Comprehensive literature review and statistical considerations for GWAS meta-analysis. Nucleic Acids Res 2012, 40(9):3777-3784.
• [26]Chen G, Wang Z, Wang D, Qiu C, Liu M, Chen X, Zhang Q, Yan G, Cui Q: LncRNADisease: a database for long-non-coding RNA-associated diseases. Nucleic Acids Res 2013, 41(Database issue):D983-D986.
• [27]Yang JH, Li JH, Jiang S, Zhou H, Qu LH: ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. Nucleic Acids Res 2013, 41(Database issue):D177-D187.
• [28]Ziebarth JD, Bhattacharya A, Chen A, Cui Y: PolymiRTS Database 2.0: linking polymorphisms in microRNA target sites with human diseases and complex traits. Nucleic Acids Res 2012, 40(Database issue):D216-D221.
• [29]Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabasi AL: The human disease network. Proc Natl Acad Sci U S A 2007, 104(21):8685-8690.
• [30]Eeles RA, Kote-Jarai Z, Giles GG, Olama AA, Guy M, Jugurnauth SK, Mulholland S, Leongamornlert DA, Edwards SM, Morrison J, Field HI, Southey MC, Severi G, Donovan JL, Hamdy FC, Dearnaley DP, Muir KR, Smith C, Bagnato M, Ardern-Jones AT, Hall AL, O'Brien LT, Gehr-Swain BN, Wilkinson RA, Cox A, Lewis S, Brown PM, Jhavar SG, Tymrakiewicz M, Lophatananon A, et al.: Multiple newly identified loci associated with prostate cancer susceptibility. Nat Genet 2008, 40(3):316-321.
• [31]Prensner JR, Iyer MK, Balbin OA, Dhanasekaran SM, Cao Q, Brenner JC, Laxman B, Asangani IA, Grasso CS, Kominsky HD, Cao X, Jing X, Wang X, Siddiqui J, Wei JT, Robinson D, Iyer HK, Palanisamy N, Maher CA, Chinnaiyan AM: Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol 2011, 29(8):742-749.