ArticleBioinformatics (Oxford, England)2021
TreeMap: a structured approach to fine mapping of eQTL variants.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 10 citations in OpenAlex.
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- Fine-mapping methods for complex traits: essential adaptations for samples of related individuals.Briefings in bioinformatics · 2025Article
- reg-eQTL: Integrating transcription factor effects to unveil regulatory variants.American journal of human genetics · 2025Article
- Identification of BCL3 as a biomarker for chondrocyte programmed cell death in osteoarthritis.International journal of experimental pathology · 2025Article
- Exploring Biomarkers Related to Cell Adhesion in Polycystic Ovary Syndrome Using Bioinformatics and Conducting Experimental Validation.International journal of general medicine · 2025Article
- Graph Visualization: Alternative Models Inspired by Bioinformatics.Sensors (Basel, Switzerland) · 2023Review
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- Bioinformatic approach for the discovery of cis-eQTL signals during fruit ripening of a woody species as grape (Vitis vinifera L.).Scientific reports · 2022Article
- Methods for statistical fine-mapping and their applications to auto-immune diseases.Seminars in immunopathology · 2022Review
- Identification of a Methylation-Regulating Genes Prognostic Signature to Predict the Prognosis and Aid Immunotherapy of Clear Cell Renal Cell Carcinoma.Frontiers in cell and developmental biology · 2022Article
- BCL2A1 and CCL18 Are Predictive Biomarkers of Cisplatin Chemotherapy and Immunotherapy in Colon Cancer Patients.Frontiers in cell and developmental biology · 2021Article
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 2 countries.
Funding
Abstract
motivationExpression quantitative trait loci (eQTL) harbor genetic variants modulating gene transcription. Fine mapping of regulatory variants at these loci is a daunting task due to the juxtaposition of causal and linked variants at a locus as well as the likelihood of interactions among multiple variants. This problem is exacerbated in genes with multiple cis-acting eQTL, where superimposed effects of adjacent loci further distort the association signals.
resultsWe developed a novel algorithm, TreeMap, that identifies putative causal variants in cis-eQTL accounting for multisite effects and genetic linkage at a locus. Guided by the hierarchical structure of linkage disequilibrium, TreeMap performs an organized search for individual and multiple causal variants. Via extensive simulations, we show that TreeMap detects co-regulating variants more accurately than current methods. Furthermore, its high computational efficiency enables genome-wide analysis of long-range eQTL. We applied TreeMap to GTEx data of brain hippocampus samples and transverse colon samples to search for eQTL in gene bodies and in 4 Mbps gene-flanking regions, discovering numerous distal eQTL. Furthermore, we found concordant distal eQTL that were present in both brain and colon samples, implying long-range regulation of gene expression. AVAILABILITY AND IMPLEMENTATION: TreeMap is available as an R package enabled for parallel processing at https://github.com/liliulab/treemap. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.