GeneSetCluster 2.0: a comprehensive toolset for summarizing and integrating gene-sets analysis
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| Publicado en: | BMC Bioinformatics vol. 26 (2025), p. 1-18 |
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| Autor principal: | |
| Otros Autores: | , , , , , , , , , |
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Springer Nature B.V.
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| Acceso en línea: | Citation/Abstract Full Text Full Text - PDF |
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| 003 | UK-CbPIL | ||
| 022 | |a 1471-2105 | ||
| 024 | 7 | |a 10.1186/s12859-025-06249-3 |2 doi | |
| 035 | |a 3247098082 | ||
| 045 | 2 | |b d20250101 |b d20251231 | |
| 084 | |a 58459 |2 nlm | ||
| 100 | 1 | |a Ortega-Legarreta, Asier | |
| 245 | 1 | |a GeneSetCluster 2.0: a comprehensive toolset for summarizing and integrating gene-sets analysis | |
| 260 | |b Springer Nature B.V. |c 2025 | ||
| 513 | |a Journal Article | ||
| 520 | 3 | |a Section BackgroundGene-Set Analysis (GSA) is commonly used to analyze high-throughput experiments. However, GSA cannot readily disentangle clusters or pathways due to redundancies in upstream knowledge bases, which hinders comprehensive exploration and interpretation of biological findings. To address this challenge, we developed GeneSetCluster, an R package designed to summarize and integrate GSA results. Over time, we and users as well identified limitations in the original version, such as difficulties in managing redundancies across multiple gene-sets, large computational times, and its lack of accessibility for users without programming expertise.AbstractSection ResultsWe present GeneSetCluster 2.0, a comprehensive upgrade that delivers methodological, computational, interpretative, and user-experience enhancements. Methodologically, GeneSetCluster 2.0 introduces a novel approach to address duplicated gene-sets and implements a seriation-based clustering algorithm that reorders results, aiding pattern identification. Computationally, the package is optimized for parallel processing, significantly reducing execution time. GeneSetCluster 2.0 enhances cluster annotations by associating clusters with relevant tissues and biological processes to improve biological interpretation, particularly for human and mouse data. To broaden accessibility, we have developed a user-friendly web application enabling non-programmers to use it. This version also ensures seamless integration between the R package, catering to users with programming expertise, and the web application for broader audiences. We evaluated the updates in a single-cell RNA public dataset.AbstractSection ConclusionGeneSetCluster 2.0 offers substantial improvements over its predecessor. Furthermore, by bridging the gap between bioinformaticians and clinicians in multidisciplinary teams, GeneSetCluster 2.0 facilitates collaborative research. The R package and web application, along with detailed installation and usage guides, are available on GitHub (https://github.com/TranslationalBioinformaticsUnit/GeneSetCluster2.0), and the web application can be accessed at https://translationalbio.shinyapps.io/genesetcluster/. | |
| 653 | |a DNA methylation | ||
| 653 | |a Parallel processing | ||
| 653 | |a Accessibility | ||
| 653 | |a Gene expression | ||
| 653 | |a Knowledge bases (artificial intelligence) | ||
| 653 | |a Applications programs | ||
| 653 | |a Bioinformatics | ||
| 653 | |a Ontology | ||
| 653 | |a Clustering | ||
| 653 | |a Databases | ||
| 653 | |a Knowledge management | ||
| 653 | |a User experience | ||
| 653 | |a Computer applications | ||
| 653 | |a Methods | ||
| 653 | |a Annotations | ||
| 653 | |a Biological activity | ||
| 653 | |a Environmental | ||
| 700 | 1 | |a Maillo, Alberto | |
| 700 | 1 | |a Mouzo, Daniel | |
| 700 | 1 | |a Ana Rosa López-Pérez | |
| 700 | 1 | |a Kular, Lara | |
| 700 | 1 | |a Majid Pahlevan Kakhki | |
| 700 | 1 | |a Jagodic, Maja | |
| 700 | 1 | |a Tegner, Jesper | |
| 700 | 1 | |a Lagani, Vincenzo | |
| 700 | 1 | |a Ewing, Ewoud | |
| 700 | 1 | |a Gomez-Cabrero, David | |
| 773 | 0 | |t BMC Bioinformatics |g vol. 26 (2025), p. 1-18 | |
| 786 | 0 | |d ProQuest |t Health & Medical Collection | |
| 856 | 4 | 1 | |3 Citation/Abstract |u https://www.proquest.com/docview/3247098082/abstract/embedded/7BTGNMKEMPT1V9Z2?source=fedsrch |
| 856 | 4 | 0 | |3 Full Text |u https://www.proquest.com/docview/3247098082/fulltext/embedded/7BTGNMKEMPT1V9Z2?source=fedsrch |
| 856 | 4 | 0 | |3 Full Text - PDF |u https://www.proquest.com/docview/3247098082/fulltextPDF/embedded/7BTGNMKEMPT1V9Z2?source=fedsrch |