SNP@lincTFBS: An Integrated Database of Polymorphisms in Human LincRNA Transcription Factor Binding Sites

PLoS One

Peng Wang¹  Tingting Wang¹  Jingrun Ye¹  Xia Li¹  Zuxianglan Zhao¹  Shangwei Ning¹  Hui Zhi¹  Ronghong Li¹  Lihua Wang²  Jianjian Wang² 

[1] College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China;The Second Affiliated Hospital, Harbin Medical University, Harbin, China

关键词: Long non-coding RNAs;    Transcription factors;    Promoter regions;    Database searching;    Nasopharyngeal carcinoma;    DNA transcription;    Genomic databases;    Molecular genetics;   

DOI  :  10.1371/journal.pone.0103851

学科分类：医学（综合）

来源: Public Library of Science

【 摘 要 】

Large intergenic non-coding RNAs (lincRNAs) are a new class of functional transcripts, and aberrant expression of lincRNAs was associated with several human diseases. The genetic variants in lincRNA transcription factor binding sites (TFBSs) can change lincRNA expression, thereby affecting the susceptibility to human diseases. To identify and annotate these functional candidates, we have developed a database SNP@lincTFBS, which is devoted to the exploration and annotation of single nucleotide polymorphisms (SNPs) in potential TFBSs of human lincRNAs. We identified 6,665 SNPs in 6,614 conserved TFBSs of 2,423 human lincRNAs. In addition, with ChIPSeq dataset, we identified 139,576 SNPs in 304,517 transcription factor peaks of 4,813 lincRNAs. We also performed comprehensive annotation for these SNPs using 1000 Genomes Project datasets across 11 populations. Moreover, one of the distinctive features of SNP@lincTFBS is the collection of disease-associated SNPs in the lincRNA TFBSs and SNPs in the TFBSs of disease-associated lincRNAs. The web interface enables both flexible data searches and downloads. Quick search can be query of lincRNA name, SNP identifier, or transcription factor name. SNP@lincTFBS provides significant advances in identification of disease-associated lincRNA variants and improved convenience to interpret the discrepant expression of lincRNAs. The SNP@lincTFBS database is available at http://bioinfo.hrbmu.edu.cn/SNP_lincTFBS.

【 授权许可】

CC BY