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.

Transcriptional regulatory regions of lncRNAs

Data statistical table

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

Contact us

Principal Investigator:Chunquan Li, Ph.D.

Phone: 86-459-8153035

Fax: 86-459-8153035

Email: lcqbio@163.com

School of Medical Informatics,Daqing Campus Harbin Medical University 39 Xinyang Road, Daqing 163319, China

Visitors

Sister Projects

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

KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription factors

ENdb: An experimentally supported enhancer database for human and mouse

Publication

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