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QTLbase: an integrative resource for quantitative trait loci across multiple human molecular phenotypes

Recent advances in genome sequencing and functional genomic profiling have promoted many large-scale quantitative trait locus (QTL) studies, which connect genotypes with tissue/cell type-specific cellular functions from transcriptional to post-translational level. However, no comprehensive resource...

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Autores principales: Zheng, Zhanye, Huang, Dandan, Wang, Jianhua, Zhao, Ke, Zhou, Yao, Guo, Zhenyang, Zhai, Sinan, Xu, Hang, Cui, Hui, Yao, Hongcheng, Wang, Zhao, Yi, Xianfu, Zhang, Shijie, Sham, Pak Chung, Li, Mulin Jun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6943073/
https://www.ncbi.nlm.nih.gov/pubmed/31598699
http://dx.doi.org/10.1093/nar/gkz888
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author Zheng, Zhanye
Huang, Dandan
Wang, Jianhua
Zhao, Ke
Zhou, Yao
Guo, Zhenyang
Zhai, Sinan
Xu, Hang
Cui, Hui
Yao, Hongcheng
Wang, Zhao
Yi, Xianfu
Zhang, Shijie
Sham, Pak Chung
Li, Mulin Jun
author_facet Zheng, Zhanye
Huang, Dandan
Wang, Jianhua
Zhao, Ke
Zhou, Yao
Guo, Zhenyang
Zhai, Sinan
Xu, Hang
Cui, Hui
Yao, Hongcheng
Wang, Zhao
Yi, Xianfu
Zhang, Shijie
Sham, Pak Chung
Li, Mulin Jun
author_sort Zheng, Zhanye
collection PubMed
description Recent advances in genome sequencing and functional genomic profiling have promoted many large-scale quantitative trait locus (QTL) studies, which connect genotypes with tissue/cell type-specific cellular functions from transcriptional to post-translational level. However, no comprehensive resource can perform QTL lookup across multiple molecular phenotypes and investigate the potential cascade effect of functional variants. We developed a versatile resource, named QTLbase, for interpreting the possible molecular functions of genetic variants, as well as their tissue/cell-type specificity. Overall, QTLbase has five key functions: (i) curating and compiling genome-wide QTL summary statistics for 13 human molecular traits from 233 independent studies; (ii) mapping QTL-relevant tissue/cell types to 78 unified terms according to a standard anatomogram; (iii) normalizing variant and trait information uniformly, yielding >170 million significant QTLs; (iv) providing a rich web client that enables phenome- and tissue-wise visualization; and (v) integrating the most comprehensive genomic features and functional predictions to annotate the potential QTL mechanisms. QTLbase provides a one-stop shop for QTL retrieval and comparison across multiple tissues and multiple layers of molecular complexity, and will greatly help researchers interrogate the biological mechanism of causal variants and guide the direction of functional validation. QTLbase is freely available at http://mulinlab.org/qtlbase.
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spelling pubmed-69430732020-01-08 QTLbase: an integrative resource for quantitative trait loci across multiple human molecular phenotypes Zheng, Zhanye Huang, Dandan Wang, Jianhua Zhao, Ke Zhou, Yao Guo, Zhenyang Zhai, Sinan Xu, Hang Cui, Hui Yao, Hongcheng Wang, Zhao Yi, Xianfu Zhang, Shijie Sham, Pak Chung Li, Mulin Jun Nucleic Acids Res Database Issue Recent advances in genome sequencing and functional genomic profiling have promoted many large-scale quantitative trait locus (QTL) studies, which connect genotypes with tissue/cell type-specific cellular functions from transcriptional to post-translational level. However, no comprehensive resource can perform QTL lookup across multiple molecular phenotypes and investigate the potential cascade effect of functional variants. We developed a versatile resource, named QTLbase, for interpreting the possible molecular functions of genetic variants, as well as their tissue/cell-type specificity. Overall, QTLbase has five key functions: (i) curating and compiling genome-wide QTL summary statistics for 13 human molecular traits from 233 independent studies; (ii) mapping QTL-relevant tissue/cell types to 78 unified terms according to a standard anatomogram; (iii) normalizing variant and trait information uniformly, yielding >170 million significant QTLs; (iv) providing a rich web client that enables phenome- and tissue-wise visualization; and (v) integrating the most comprehensive genomic features and functional predictions to annotate the potential QTL mechanisms. QTLbase provides a one-stop shop for QTL retrieval and comparison across multiple tissues and multiple layers of molecular complexity, and will greatly help researchers interrogate the biological mechanism of causal variants and guide the direction of functional validation. QTLbase is freely available at http://mulinlab.org/qtlbase. Oxford University Press 2020-01-08 2019-10-10 /pmc/articles/PMC6943073/ /pubmed/31598699 http://dx.doi.org/10.1093/nar/gkz888 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Database Issue
Zheng, Zhanye
Huang, Dandan
Wang, Jianhua
Zhao, Ke
Zhou, Yao
Guo, Zhenyang
Zhai, Sinan
Xu, Hang
Cui, Hui
Yao, Hongcheng
Wang, Zhao
Yi, Xianfu
Zhang, Shijie
Sham, Pak Chung
Li, Mulin Jun
QTLbase: an integrative resource for quantitative trait loci across multiple human molecular phenotypes
title QTLbase: an integrative resource for quantitative trait loci across multiple human molecular phenotypes
title_full QTLbase: an integrative resource for quantitative trait loci across multiple human molecular phenotypes
title_fullStr QTLbase: an integrative resource for quantitative trait loci across multiple human molecular phenotypes
title_full_unstemmed QTLbase: an integrative resource for quantitative trait loci across multiple human molecular phenotypes
title_short QTLbase: an integrative resource for quantitative trait loci across multiple human molecular phenotypes
title_sort qtlbase: an integrative resource for quantitative trait loci across multiple human molecular phenotypes
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6943073/
https://www.ncbi.nlm.nih.gov/pubmed/31598699
http://dx.doi.org/10.1093/nar/gkz888
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