Master regulator activity QTL protocol to implicate regulatory pathways potentially mediating GWAS signals using eQTL data
Summary: Here, we present a protocol to identify transcriptional regulators potentially mediating downstream biological effects of germline variants associated with complex traits of interest, which enables functional hypothesis generation independent of colocalizing expression quantitative trait lo...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-09-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166723003295 |
| _version_ | 1797801682845827072 |
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| author | Jason W. Hoskins Trevor A. Christensen Laufey T. Amundadottir |
| author_facet | Jason W. Hoskins Trevor A. Christensen Laufey T. Amundadottir |
| author_sort | Jason W. Hoskins |
| collection | DOAJ |
| description | Summary: Here, we present a protocol to identify transcriptional regulators potentially mediating downstream biological effects of germline variants associated with complex traits of interest, which enables functional hypothesis generation independent of colocalizing expression quantitative trait loci (eQTLs). We describe steps for tissue-/cell-type-specific co-expression network modeling, expression regulator activity inference, and identification of representative phenotypic master regulators. Finally, we detail activity QTL and eQTL analyses. This protocol requires genotype, expression, and relevant covariables and phenotype data from existing eQTL datasets.For complete details on the use and execution of this protocol, please refer to Hoskins et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-03-13T04:54:12Z |
| format | Article |
| id | doaj.art-0bc58f92ecd7406c9bcf7c850e988d04 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-03-13T04:54:12Z |
| publishDate | 2023-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-0bc58f92ecd7406c9bcf7c850e988d042023-06-18T05:03:19ZengElsevierSTAR Protocols2666-16672023-09-0143102362Master regulator activity QTL protocol to implicate regulatory pathways potentially mediating GWAS signals using eQTL dataJason W. Hoskins0Trevor A. Christensen1Laufey T. Amundadottir2Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MA 20892, USA; Corresponding authorLaboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MA 20892, USALaboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MA 20892, USA; Corresponding authorSummary: Here, we present a protocol to identify transcriptional regulators potentially mediating downstream biological effects of germline variants associated with complex traits of interest, which enables functional hypothesis generation independent of colocalizing expression quantitative trait loci (eQTLs). We describe steps for tissue-/cell-type-specific co-expression network modeling, expression regulator activity inference, and identification of representative phenotypic master regulators. Finally, we detail activity QTL and eQTL analyses. This protocol requires genotype, expression, and relevant covariables and phenotype data from existing eQTL datasets.For complete details on the use and execution of this protocol, please refer to Hoskins et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166723003295BioinformaticsGeneticsGenomicsRNAseqGene ExpressionSystems Biology |
| spellingShingle | Jason W. Hoskins Trevor A. Christensen Laufey T. Amundadottir Master regulator activity QTL protocol to implicate regulatory pathways potentially mediating GWAS signals using eQTL data STAR Protocols Bioinformatics Genetics Genomics RNAseq Gene Expression Systems Biology |
| title | Master regulator activity QTL protocol to implicate regulatory pathways potentially mediating GWAS signals using eQTL data |
| title_full | Master regulator activity QTL protocol to implicate regulatory pathways potentially mediating GWAS signals using eQTL data |
| title_fullStr | Master regulator activity QTL protocol to implicate regulatory pathways potentially mediating GWAS signals using eQTL data |
| title_full_unstemmed | Master regulator activity QTL protocol to implicate regulatory pathways potentially mediating GWAS signals using eQTL data |
| title_short | Master regulator activity QTL protocol to implicate regulatory pathways potentially mediating GWAS signals using eQTL data |
| title_sort | master regulator activity qtl protocol to implicate regulatory pathways potentially mediating gwas signals using eqtl data |
| topic | Bioinformatics Genetics Genomics RNAseq Gene Expression Systems Biology |
| url | http://www.sciencedirect.com/science/article/pii/S2666166723003295 |
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