GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets DOI Creative Commons
Giacomo B. Marino, Stephanie Olaiya, John Erol Evangelista

et al.

GigaScience, Journal Year: 2025, Volume and Issue: 14

Published: Jan. 1, 2025

Abstract Converting multiomics datasets into gene sets facilitates data integration that leads to knowledge discovery. Although there are tools developed analyze sets, only a few offer the management of from multiple sources. GeneSetCart is an interactive web-based platform enables investigators gather various sources; augment these with gene–gene coexpression correlations and protein–protein interactions; perform set operations on such as union, consensus, intersection; visualize all in one place. supports upload single or well fetching by searching PubMed for genes comentioned terms publications. Venn diagrams, heatmaps, Uniform Manifold Approximation Projection (UMAP) plots, SuperVenn UpSet plots can session summarize similarity overlap among sets. Users also enrichment analysis their assembled external tools. All be saved user account reanalysis sharing collaborators. has library crossing feature created several National Institutes Health Common Fund programs. For top overlapping pairs programs, large language model (LLM) prompted propose possible reasons high overlap. Using this feature, two use cases presented. In addition, users produce publication-ready reports uploaded Text supplemented LLM. Overall, useful resource enabling biologists without programming expertise facilitate hypothesis generation.

Language: Английский

GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets DOI Creative Commons
Giacomo B. Marino, Stephanie Olaiya, John Erol Evangelista

et al.

GigaScience, Journal Year: 2025, Volume and Issue: 14

Published: Jan. 1, 2025

Abstract Converting multiomics datasets into gene sets facilitates data integration that leads to knowledge discovery. Although there are tools developed analyze sets, only a few offer the management of from multiple sources. GeneSetCart is an interactive web-based platform enables investigators gather various sources; augment these with gene–gene coexpression correlations and protein–protein interactions; perform set operations on such as union, consensus, intersection; visualize all in one place. supports upload single or well fetching by searching PubMed for genes comentioned terms publications. Venn diagrams, heatmaps, Uniform Manifold Approximation Projection (UMAP) plots, SuperVenn UpSet plots can session summarize similarity overlap among sets. Users also enrichment analysis their assembled external tools. All be saved user account reanalysis sharing collaborators. has library crossing feature created several National Institutes Health Common Fund programs. For top overlapping pairs programs, large language model (LLM) prompted propose possible reasons high overlap. Using this feature, two use cases presented. In addition, users produce publication-ready reports uploaded Text supplemented LLM. Overall, useful resource enabling biologists without programming expertise facilitate hypothesis generation.

Language: Английский

Citations

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