Here, we developed a comprehensive database of human transcriptional regulation of lncRNAs (TRlnc, http://bio.licpathway.net/TRlnc), which aims to collect a large number of available resources of transcriptional regulatory regions of lncRNAs, and to annotate and illustrate their potential roles in the regulation of lncRNAs in cell type-specific manner.
The current version of TRlnc contains 8,683,028 typical enhancers/super-enhancers and 32,348,244 chromatin accessibility regions associated with 91,906 human lncRNAs. These regions were identified from over 900 human H3K27ac ChIP-seq, ATAC-seq and DNase-seq samples. Furthermore, TRlnc provides the detailed (epi) genetic information in transcriptional regulatory regions (promoter, enhancer/super-enhancer and chromatin accessibility regions) of lncRNAs, including common SNPs, Risk SNPs, eQTLs, Linkage disequilibrium SNPs, TFs predicted by motifs, TFs identified by ChIP-seq, methylation sites of 450K array, methylation sites of whole-genome shotgun bisulfite sequencing, histone modifications and 3D chromatin interactions, especially supporting the display of TFs binding to transcriptional regulatory regions from over 7,000 TF ChIP-seq samples. In addition, TRlnc integrates miRNAs, diseases, expression, localization and proteins associated with lncRNAs from multiple sources.
|LncRNA||Number in GENCODE||13,523|
|Number in NONCODE||78,383|
|ChIP-seq||Number of Sources||4|
|Number of Samples||542|
|Number of Regions||8,684,552|
|ATAC-seq||Number of Sources||2|
|Number of Samples||128|
|Number of Regions||5,939,835|
|DNase-seq||Number of Sources||3|
|Number of Samples||290|
|Number of Regions||26,408,409|
Principal Investigator:Chunquan Li, Ph.D.
School of Medical Informatics,Daqing Campus Harbin Medical University 39 Xinyang Road, Daqing 163319, China
TRCirc: a resource for transcriptional regulation information of circRNAs
SEdb: The comprehensive human Super-Enhancer database
SEanalysis: A web tool for super-enhancer associated regulatory analysis
Yanyu Li, Xuecang Li, Yongsan Yang, Meng Li, Fengcui Qian, Zhidong Tang, Jianmei Zhao, Jian Zhang, Xuefeng Bai, Yong Jiang, Jianyuan Zhou, Yuexin Zhang, Liwei Zhou, Jianjun Xie, Enmin Li, Qiuyu Wang, Chunquan Li, TRlnc: a comprehensive database for human transcriptional regulatory information of lncRNAs, Briefings in Bioinformatics, , bbaa011, https://doi.org/10.1093/bib/bbaa011