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Types of Cis- and Trans-Gene Regulation of Expression Quantitative Trait Loci Across Human Tissues

Jarred Kvamme, Md Bahadur Badsha, Evan A. Martin, Jiayu Wu, Mohamed Megheib, Xiaoyue Wang, View ORCID ProfileAudrey Qiuyan Fu
doi: https://doi.org/10.1101/2022.01.24.477617
Jarred Kvamme
1The Bioinformatics and Computational Biology Program, University of Idaho
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Md Bahadur Badsha
2Institute for Modeling Collaboration and Innovation, University of Idaho
6Center for Applied Bioinformatics, St. Jude Children’s Research Hospital
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Evan A. Martin
1The Bioinformatics and Computational Biology Program, University of Idaho
7Pacific Northwest National Laboratory
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Jiayu Wu
3Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences
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Mohamed Megheib
1The Bioinformatics and Computational Biology Program, University of Idaho
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Xiaoyue Wang
3Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences
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Audrey Qiuyan Fu
1The Bioinformatics and Computational Biology Program, University of Idaho
2Institute for Modeling Collaboration and Innovation, University of Idaho
4Institute for Interdisciplinary Data Sciences, University of Idaho
5Department of Mathematics and Statistical Science, University of Idaho
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  • ORCID record for Audrey Qiuyan Fu
  • For correspondence: audreyf@uidaho.edu
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Abstract

Expression quantitative trait loci (eQTLs) have been identified for most genes in the human genome across nearly 50 tissues or cell types. While most of the eQTLs are near the associated genes, some can be far away or on different chromosomes, with the regulatory mechanisms largely unknown. Here, we study cis- and trans-regulation of eQTLs across multiple tissues and cell types. Specifically, we constructed trios consisting of an eQTL, its cis-gene and trans-gene and inferred the regulatory relationships with causal network inference. We identify multiple types of regulatory networks for trios: across all the tissues, more than half of the trios are inferred to be conditionally independent, where the two genes are conditionally independent given the genotype of the eQTL (cis-gene ← eQTL → trans-gene). Around 1.5% of the trios are inferred to be mediation (eQTL → mediator → target), around 1.3% fully connected among the three nodes, and just a handful v-structures (eQTL → gene 1 ← gene 2). Unexpectedly, across the tissues, on average more than half of the mediation trios have the trans-gene as the mediator. Most of the mediators (cis and trans) are tissue specific. Furthermore, cis-gene mediators are significantly enriched for protein-coding genes compared with the genome average, whereas trans-gene mediators are significantly enriched for pseudogenes and depleted for long noncoding RNAs (lncRNAs).

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted January 25, 2022.
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Types of Cis- and Trans-Gene Regulation of Expression Quantitative Trait Loci Across Human Tissues
Jarred Kvamme, Md Bahadur Badsha, Evan A. Martin, Jiayu Wu, Mohamed Megheib, Xiaoyue Wang, Audrey Qiuyan Fu
bioRxiv 2022.01.24.477617; doi: https://doi.org/10.1101/2022.01.24.477617
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Types of Cis- and Trans-Gene Regulation of Expression Quantitative Trait Loci Across Human Tissues
Jarred Kvamme, Md Bahadur Badsha, Evan A. Martin, Jiayu Wu, Mohamed Megheib, Xiaoyue Wang, Audrey Qiuyan Fu
bioRxiv 2022.01.24.477617; doi: https://doi.org/10.1101/2022.01.24.477617

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