LncBRAIN: a database for eQTL lncRNAs in human brain
The samples of LncBRAIN are from UK Brain Expression Consortium (UKBEC) involving in ten brain regions, i.e. CRBL: cerebellar cortex, FCTX: frontal cortex, HIPP: hippocampus, MEDU: medulla (specifically inferior olivary nucleus), OCTX: occipital cortex (specifically primary visual cortex), PUTM: putamen, SNIG: substantia nigra, TCTX: temporal cortex, THAL: thalamus, WHMT: intralobular white matter.
LncBRAIN provides comprehensive information of lncRNA expression regulation across ten human brain regions. In LncRNAs and SNPs module, users can input the Ensemble ID to visualize the expression patterns of individual lncRNAs across various genders and age groups in ten distinct brain regions. Age categories are delineated as follows: children (0-18 years), adolescents (19-44 years), middle-aged adults (45-59 years), and elderly individuals (≥ 60 years). Furthermore, the linkage disequilibrium (LD) map of variants within the cis-region (within 1 Mb around the transcriptional start site) of individual lncRNAs. Moreover, by entering the SNP ID within the cis-region of the queried lncRNA, users can obtain the eQTL results in the ten brain regions, i.e, the expression profile of the lncRNA across different genotypes of this variant. Additionally, in Download module, we provided the complete cis-eQTL results and the genome-wide eQTL results (including tran-eQTLs) with a limiting threshold of P < 10-5 across ten brain regions. We also offered genetic prediction models trained using PredictDB in this module, which can be used in combination with GWAS data to perform further TWAS analysis for lncRNAs by the third-party tools (e.g., MetaXcan).
LncRNAs and SNPs
This module provides the expression of lncRNAs and the information of eQTLs and SNP linkage disequilibrium (LD) map in cis-regions (within 1 Mb around the TSS of lncRNAs) across the ten brain tissues. The information of trans-eQTLs can be downlowded from the “Download Data” module.
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Expression Level
Expression Level according to Gender
Expression Level according to Age
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LncRNA expression(0:Female;1:Male)
- CRBL_lncRNA.txt
- FCTX_lncRNA.txt
- HIPP_lncRNA.txt
- MEDU_lncRNA.txt
- OCTX_lncRNA.txt
- PUTM_lncRNA.txt
- SNIG_lncRNA.txt
- TCTX_lncRNA.txt
- THAL_lncRNA.txt
- WHMT_lncRNA.txt
Complete cis-eQTL results
- CRBL-cis-eQTL.txt
- FCTX-cis-eQTL.txt
- HIPP-cis-eQTL.txt
- MEDU-cis-eQTL.txt
- OCTX-cis-eQTL.txt
- PUTM-cis-eQTL.txt
- SNIG-cis-eQTL.txt
- TCTX-cis-eQTL.txt
- THAL-cis-eQTL.txt
- WHMT-cis-eQTL.txt
Genome-wide eQTL results (including tran-eQTLs) with a limiting threshold of P < 10-5
- CRBL-sig-eQTL.txt
- FCTX-sig-eQTL.txt
- HIPP-sig-eQTL.txt
- MEDU-sig-eQTL.txt
- OCTX-sig-eQTL.txt
- PUTM-sig-eQTL.txt
- SNIG-sig-eQTL.txt
- TCTX-sig-eQTL.txt
- THAL-sig-eQTL.txt
- WHMT-sig-eQTL.txt
Genetic prediction models (.db) and covariance matrices (.txt)
How to use this site?
| NAME | ORGANIZATION | EMAIL ADDRESS |
|---|---|---|
| Zhijie Han | ChongQing Medical University | zhijiehan@cqu.edu.cn |
| Yijie He | ChongQing Medical University | heyijie456@163.com |
| Yaqin Tang | ChongQing Medical University | yqtang@cqmu.edu.cn |
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