Gene Set Analysis: Challenges, Opportunities, and Future Research
Gene set analysis methods are widely used to provide insight into high-throughput gene expression data. There are many gene set analysis methods available. These methods rely on various assumptions and have different requirements, strengths and weaknesses. In this paper, we classify gene set analysi...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-06-01
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| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2020.00654/full |
| _version_ | 1818945004514574336 |
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| author | Farhad Maleki Katie Ovens Daniel J. Hogan Anthony J. Kusalik |
| author_facet | Farhad Maleki Katie Ovens Daniel J. Hogan Anthony J. Kusalik |
| author_sort | Farhad Maleki |
| collection | DOAJ |
| description | Gene set analysis methods are widely used to provide insight into high-throughput gene expression data. There are many gene set analysis methods available. These methods rely on various assumptions and have different requirements, strengths and weaknesses. In this paper, we classify gene set analysis methods based on their components, describe the underlying requirements and assumptions for each class, and provide directions for future research in developing and evaluating gene set analysis methods. |
| first_indexed | 2024-12-20T07:52:13Z |
| format | Article |
| id | doaj.art-41ac4be7e0b84778ba2f4ccd71bb22d0 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-20T07:52:13Z |
| publishDate | 2020-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-41ac4be7e0b84778ba2f4ccd71bb22d02022-12-21T19:47:47ZengFrontiers Media S.A.Frontiers in Genetics1664-80212020-06-011110.3389/fgene.2020.00654531777Gene Set Analysis: Challenges, Opportunities, and Future ResearchFarhad MalekiKatie OvensDaniel J. HoganAnthony J. KusalikGene set analysis methods are widely used to provide insight into high-throughput gene expression data. There are many gene set analysis methods available. These methods rely on various assumptions and have different requirements, strengths and weaknesses. In this paper, we classify gene set analysis methods based on their components, describe the underlying requirements and assumptions for each class, and provide directions for future research in developing and evaluating gene set analysis methods.https://www.frontiersin.org/article/10.3389/fgene.2020.00654/fullgene expressiongene set analysisgene set enrichmentgene set databasesensitivityspecificity |
| spellingShingle | Farhad Maleki Katie Ovens Daniel J. Hogan Anthony J. Kusalik Gene Set Analysis: Challenges, Opportunities, and Future Research Frontiers in Genetics gene expression gene set analysis gene set enrichment gene set database sensitivity specificity |
| title | Gene Set Analysis: Challenges, Opportunities, and Future Research |
| title_full | Gene Set Analysis: Challenges, Opportunities, and Future Research |
| title_fullStr | Gene Set Analysis: Challenges, Opportunities, and Future Research |
| title_full_unstemmed | Gene Set Analysis: Challenges, Opportunities, and Future Research |
| title_short | Gene Set Analysis: Challenges, Opportunities, and Future Research |
| title_sort | gene set analysis challenges opportunities and future research |
| topic | gene expression gene set analysis gene set enrichment gene set database sensitivity specificity |
| url | https://www.frontiersin.org/article/10.3389/fgene.2020.00654/full |
| work_keys_str_mv | AT farhadmaleki genesetanalysischallengesopportunitiesandfutureresearch AT katieovens genesetanalysischallengesopportunitiesandfutureresearch AT danieljhogan genesetanalysischallengesopportunitiesandfutureresearch AT anthonyjkusalik genesetanalysischallengesopportunitiesandfutureresearch |