title: SNP@lincTFBS: an integrated database of polymorphisms in human LincRNA transcription factor binding sites.
abstract: 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.
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors: Shangwei
authors: S
authors: Ning
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors: Zuxianglan
authors: Z
authors: Zhao
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors: Jingrun
authors: J
authors: Ye
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors: Peng
authors: P
authors: Wang
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors: Hui
authors: H
authors: Zhi
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors: Ronghong
authors: R
authors: Li
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors: Tingting
authors: T
authors: Wang
authors: The Second Affiliated Hospital, Harbin Medical University, Harbin, China.
authors: Jianjian
authors: J
authors: Wang
authors: The Second Affiliated Hospital, Harbin Medical University, Harbin, China.
authors: Lihua
authors: L
authors: Wang
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors: Xia
authors: X
authors: Li
mesh_terms: D001665:Binding Sites; D030541:Databases, Genetic; D015894:Genome, Human; D006801:Humans; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D062085:RNA, Long Noncoding / Q000235:genetics*; D014157:Transcription Factors / Q000502:physiology*; D014584:User-Computer Interface
chemical_list: D062085:RNA, Long Noncoding; D014157:Transcription Factors