Title |
Gene Set Enrichment Analyses: lessons learned from the heart failure phenotype
|
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Published in |
BioData Mining, May 2017
|
DOI | 10.1186/s13040-017-0137-5 |
Pubmed ID | |
Authors |
Vinicius Tragante, Johannes M. I. H. Gho, Janine F. Felix, Ramachandran S. Vasan, Nicholas L. Smith, Benjamin F. Voight, CHARGE Heart Failure Working Group, Colin Palmer, Pim van der Harst, Jason H. Moore, Folkert W. Asselbergs |
Abstract |
Genetic studies for complex diseases have predominantly discovered main effects at individual loci, but have not focused on genomic and environmental contexts important for a phenotype. Gene Set Enrichment Analysis (GSEA) aims to address this by identifying sets of genes or biological pathways contributing to a phenotype, through gene-gene interactions or other mechanisms, which are not the focus of conventional association methods. Approaches that utilize GSEA can now take input from array chips, either gene-centric or genome-wide, but are highly sensitive to study design, SNP selection and pruning strategies, SNP-to-gene mapping, and pathway definitions. Here, we present lessons learned from our experience with GSEA of heart failure, a particularly challenging phenotype due to its underlying heterogeneous etiology. This case study shows that proper data handling is essential to avoid false-positive results. Well-defined pipelines for quality control are needed to avoid reporting spurious results using GSEA. |
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Geographical breakdown
Country | Count | As % |
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United States | 4 | 40% |
Malaysia | 1 | 10% |
Germany | 1 | 10% |
Unknown | 4 | 40% |
Demographic breakdown
Type | Count | As % |
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Members of the public | 5 | 50% |
Scientists | 5 | 50% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
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Unknown | 28 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
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Researcher | 9 | 32% |
Student > Ph. D. Student | 6 | 21% |
Student > Master | 3 | 11% |
Other | 2 | 7% |
Student > Bachelor | 1 | 4% |
Other | 2 | 7% |
Unknown | 5 | 18% |
Readers by discipline | Count | As % |
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Biochemistry, Genetics and Molecular Biology | 7 | 25% |
Agricultural and Biological Sciences | 7 | 25% |
Computer Science | 3 | 11% |
Medicine and Dentistry | 2 | 7% |
Pharmacology, Toxicology and Pharmaceutical Science | 1 | 4% |
Other | 2 | 7% |
Unknown | 6 | 21% |