SNP@lincTFBS: an integrated database of polymorphisms in human LincRNA transcription factor binding sites.
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 susce...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2014-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC4116217?pdf=render |
| _version_ | 1818031838509137920 |
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| author | Shangwei Ning Zuxianglan Zhao Jingrun Ye Peng Wang Hui Zhi Ronghong Li Tingting Wang Jianjian Wang Lihua Wang Xia Li |
| author_facet | Shangwei Ning Zuxianglan Zhao Jingrun Ye Peng Wang Hui Zhi Ronghong Li Tingting Wang Jianjian Wang Lihua Wang Xia Li |
| author_sort | Shangwei Ning |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-10T05:57:50Z |
| format | Article |
| id | doaj.art-5cb94b66921a4433bee66e81a3ae9285 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-10T05:57:50Z |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-5cb94b66921a4433bee66e81a3ae92852022-12-22T01:59:53ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0197e10385110.1371/journal.pone.0103851SNP@lincTFBS: an integrated database of polymorphisms in human LincRNA transcription factor binding sites.Shangwei NingZuxianglan ZhaoJingrun YePeng WangHui ZhiRonghong LiTingting WangJianjian WangLihua WangXia LiLarge 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.http://europepmc.org/articles/PMC4116217?pdf=render |
| spellingShingle | Shangwei Ning Zuxianglan Zhao Jingrun Ye Peng Wang Hui Zhi Ronghong Li Tingting Wang Jianjian Wang Lihua Wang Xia Li SNP@lincTFBS: an integrated database of polymorphisms in human LincRNA transcription factor binding sites. PLoS ONE |
| title | SNP@lincTFBS: an integrated database of polymorphisms in human LincRNA transcription factor binding sites. |
| title_full | SNP@lincTFBS: an integrated database of polymorphisms in human LincRNA transcription factor binding sites. |
| title_fullStr | SNP@lincTFBS: an integrated database of polymorphisms in human LincRNA transcription factor binding sites. |
| title_full_unstemmed | SNP@lincTFBS: an integrated database of polymorphisms in human LincRNA transcription factor binding sites. |
| title_short | SNP@lincTFBS: an integrated database of polymorphisms in human LincRNA transcription factor binding sites. |
| title_sort | snp linctfbs an integrated database of polymorphisms in human lincrna transcription factor binding sites |
| url | http://europepmc.org/articles/PMC4116217?pdf=render |
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