SNP@lincTFBS: An integrated database of polymorphisms in human lincRNA transcription factor binding sites

PLoS ONE

Volumn 9, Issue 7, 2014, Pages

  Ning, Shangwei ^a   Zhao, Zuxianglan ^a   Ye, Jingrun ^a   Wang, Peng ^a   Zhi, Hui ^a   Li, Ronghong ^a   Wang, Tingting ^a   Wang, Jianjian ^a   Wang, Lihua ^a   Li, Xia ^a  

^a HARBIN MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROXYMETHYLGLUTARYL COENZYME A REDUCTASE INHIBITOR; LINCRNA TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; URATE; LONG UNTRANSLATED RNA;

ALZHEIMER DISEASE; ARTICLE; ASTHMA; BINDING SITE; BIPOLAR DISORDER; CANCER GROWTH; CANCER PROGNOSIS; CARCINOGENESIS; CELIAC DISEASE; COMPUTER INTERFACE; CONTROLLED STUDY; DATA BASE; DISEASE ASSOCIATION; GENE; GENETIC ASSOCIATION; GENETIC CONSERVATION; GENETIC VARIABILITY; GLIOMA; HUMAN; HUMAN CELL; LINC00312; MAJOR DEPRESSION; METABOLITE; NAG7 GENE; NASOPHARYNX CARCINOMA; NEUROBLASTOMA; NON INSULIN DEPENDENT DIABETES MELLITUS; OBESITY; PROGRESSIVE SUPRANUCLEAR PALSY; RNA TRANSCRIPTION; SEARCH ENGINE; SINGLE NUCLEOTIDE POLYMORPHISM; SUICIDE ATTEMPT; URIC ACID BLOOD LEVEL; WEB BROWSER; GENETIC DATABASE; GENETICS; HUMAN GENOME; MOLECULAR GENETICS; PHYSIOLOGY;

BINDING SITES; DATABASES, GENETIC; GENOME, HUMAN; HUMANS; MOLECULAR SEQUENCE ANNOTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; RNA, LONG NONCODING; TRANSCRIPTION FACTORS; USER-COMPUTER INTERFACE;

EID: 84905027964     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0103851     Document Type: Article

References (46)

1. Ponting CP, Oliver PL, Reik W (2009) Evolution and functions of long noncoding RNAs. Cell 136: 629-641.
2. Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, et al. (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25: 1915-1927.
3. Lee JT (2012) Epigenetic regulation by long noncoding RNAs. Science 338: 1435-1439.
4. Khalil AM, Guttman M, Huarte M, Garber M, Raj A, et al. (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A 106: 11667-11672.
5. Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS (2008) Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci U S A 105: 716-721. (Pubitemid 351171774)
6. Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, et al. (2011) lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 477: 295-300.
7. Wapinski O, Chang HY (2011) Long noncoding RNAs and human disease. Trends Cell Biol 21: 354-361.
8. Maruyama R, Suzuki H (2012) Long noncoding RNA involvement in cancer. BMB Rep 45: 604-611.
9. Bialkowska-Hobrzanska H, Driman DK, 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.
10. Kumar V, Westra HJ, Karjalainen J, Zhernakova DV, Esko T, et al. (2013) Human disease-associated genetic variation impacts large intergenic non-coding RNA expression. PLoS Genet 9: e1003201.
11. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, et al. (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464: 1071-1076.
12. Nie Y, Liu X, Qu S, Song E, Zou H, et al. (2013) Long non-coding RNA HOTAIR is an independent prognostic marker for nasopharyngeal carcinoma progression and survival. Cancer Sci 104: 458-464.
13. Gutschner T, Hammerle M, Eissmann M, Hsu J, Kim Y, et al. (2013) The noncoding RNA MALAT1 is a critical regulator of the metastasis phenotype of lung cancer cells. Cancer Res 73: 1180-1189.
14. Gutschner T, Hammerle M, Diederichs S (2013) MALAT1 - a paradigm for long noncoding RNA function in cancer. J Mol Med (Berl) 91: 791-801.
15. Matouk IJ, Abbasi I, Hochberg A, Galun E, Dweik H, et al. (2009) Highly upregulated in liver cancer noncoding RNA is overexpressed in hepatic colorectal metastasis. Eur J Gastroenterol Hepatol 21: 688-692.
16. Hata J, Matsuda K, Ninomiya T, Yonemoto K, Matsushita T, et al. (2007) Functional SNP in an Sp1-binding site of AGTRL1 gene is associated with susceptibility to brain infarction. Hum Mol Genet 16: 630-639. (Pubitemid 46585664)
17. Blanton SH, Burt A, Garcia E, Mulliken JB, Stal S, et al. (2010) Ethnic Heterogeneity of IRF6 AP-2a Binding Site Promoter SNP Association With Nonsyndromic Cleft Lip and Palate. Cleft Palate Craniofac J 47: 574-577.
18. Badano I, Stietz SM, Schurr TG, Picconi AM, Fekete D, et al. (2012) Analysis of TNFalpha promoter SNPs and the risk of cervical cancer in urban populations of Posadas (Misiones, Argentina). J Clin Virol 53: 54-59.
19. Jung M, Cho BC, Lee CH, Park HS, Kang YA, et al. (2012) EGFR polymorphism as a predictor of clinical outcome in advanced lung cancer patients treated with EGFR-TKI. Yonsei Med J 53: 1128-1135.
20. Kohanbash G, Ishikawa E, Fujita M, Ikeura M, McKaveney K, et al. (2012) Differential activity of interferon-alpha8 promoter is regulated by Oct-1 and a SNP that dictates prognosis of glioma. Oncoimmunology 1: 487-492.
21. Jendrzejewski J, He H, Radomska HS, Li W, Tomsic J, et al. (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.
22. Yang Z, Zhou L,Wu LM, Lai MC, Xie HY, et al. (2011) Overexpression of long non-coding RNA HOTAIR predicts tumor recurrence in hepatocellular carcinoma patients following liver transplantation. Ann Surg Oncol 18: 1243-1250.
23. Chen G, Wang Z, Wang D, Qiu C, Liu M, et al. (2013) LncRNADisease: a database for long-non-coding RNA-associated diseases. Nucleic Acids Res 41: D983-986.
24. Yang JH, Li JH, Jiang S, Zhou H, Qu LH (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: D177-187.
25. The Wellcome Trust Case Control Consortium (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447: 661-678.
26. Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, et al. (2012) GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res 22: 1760-1774.
27. Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, et al. (2003) The UCSC Genome Browser Database. Nucleic Acids Res 31: 51-54. (Pubitemid 36150331)
28. Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, et al. (2008) The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res 36: D773-779. (Pubitemid 351149822)
29. Jarinova O, Stewart AF, Roberts R, Wells G, Lau P, et al. (2009) Functional analysis of the chromosome 9p21.3 coronary artery disease risk locus. Arterioscler Thromb Vasc Biol 29: 1671-1677.
30. Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, et al. (2009) PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol 27: 66-75.
31. Broadbent HM, Peden JF, Lorkowski S, Goel A, Ongen H, et al. (2008) Susceptibility to coronary artery disease and diabetes is encoded by distinct, tightly linked SNPs in the ANRIL locus on chromosome 9p. Hum Mol Genet 17: 806-814. (Pubitemid 351359697)
32. Barber MJ, Mangravite LM, Hyde CL, Chasman DI, Smith JD, et al. (2010) Genome-wide association of lipid-lowering response to statins in combined study populations. PLoS One 5: e9763.
33. Huang da W, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
34. Ying L, Huang Y, Chen H, Wang Y, Xia L, et al. (2013) Downregulated MEG3 activates autophagy and increases cell proliferation in bladder cancer. Mol Biosyst 9: 407-411.
35. Volders PJ, Helsens K, Wang X, Menten B, Martens L, et al. (2012) LNCipedia: a database for annotated human lncRNA transcript sequences and structures. Nucleic Acids Res 41: D246-251.
36. Prensner JR, Iyer MK, Balbin OA, Dhanasekaran SM, Cao Q, et al. (2011) Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol 29: 742-749.
37. Baldinu P, Cossu A, Manca A, Satta MP, Sini MC, et al. (2004) Identification of a novel candidate gene, CASC2, in a region of common allelic loss at chromosome 10q26 in human endometrial cancer. Hum Mutat 23: 318-326. (Pubitemid 38461513)
38. Pujana MA, Ruiz A, Badenas C, Puig-Butille JA, Nadal M, et al. (2007) Molecular characterization of a t(9;12)(p21;q13) balanced chromosome translocation in combination with integrative genomics analysis identifies C9orf14 as a candidate tumor-suppressor. Genes Chromosomes Cancer 46: 155-162. (Pubitemid 44913380)
39. Tan C, Peng C, Huang YC, Zhang QH, Tang K, et al. (2002) Effects of NPC-associated gene NAG7 on cell cycle and apoptosis in nasopharyngeal carcinoma cells. Ai Zheng 21: 449-455.
40. Gray KA, Daugherty LC, Gordon SM, Seal RL, Wright MW, et al. (2013) Genenames.org: the HGNC resources in 2013. Nucleic Acids Res 41: D545-552.
41. Zhang W, Huang C, Gong Z, Zhao Y, Tang K, et al. (2013) Expression of LINC00312, a long intergenic non-coding RNA, is negatively correlated with tumor size but positively correlated with lymph node metastasis in nasopharyngeal carcinoma. J Mol Histol 44(5): 545-554.
42. Wang P, Ren Z, Sun P (2012) Overexpression of the long non-coding RNA MEG3 impairs in vitro glioma cell proliferation. J Cell Biochem 113: 1868-1874.
43. Astuti D, Latif F, Wagner K, Gentle D, Cooper WN, et al. (2005) Epigenetic alteration at the DLK1-GTL2 imprinted domain in human neoplasia: analysis of neuroblastoma, phaeochromocytoma and Wilms' tumour. Br J Cancer 92: 1574-1580. (Pubitemid 40705027)
44. Airavaara M, Pletnikova O, Doyle ME, Zhang YE, Troncoso JC, et al. (2011) Identification of novel GDNF isoforms and cis-antisense GDNFOS gene and their regulation in human middle temporal gyrus of Alzheimer disease. J Biol Chem 286: 45093-45102.
45. Hollingworth P, Sweet R, Sims R, Harold D, Russo G, et al. (2012) Genome-wide association study of Alzheimer's disease with psychotic symptoms. Mol Psychiatry 17: 1316-1327.
46. Qureshi IA, Mattick JS, Mehler MF (2010) Long non-coding RNAs in nervous system function and disease. Brain Res 1338: 20-35.