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PANGEA: a new gene set enrichment tool for Drosophila and common research organisms

Gene set enrichment analysis (GSEA) plays an important role in large-scale data analysis, helping scientists discover the underlying biological patterns over-represented in a gene list resulting from, for example, an ‘omics’ study. Gene Ontology (GO) annotation is the most frequently used classifica...

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Autores principales: Hu, Yanhui, Comjean, Aram, Attrill, Helen, Antonazzo, Giulia, Thurmond, Jim, Chen, Weihang, Li, Fangge, Chao, Tiffany, Mohr, Stephanie E, Brown, Nicholas H, Perrimon, Norbert
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10320058/
https://www.ncbi.nlm.nih.gov/pubmed/37125646
http://dx.doi.org/10.1093/nar/gkad331
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author Hu, Yanhui
Comjean, Aram
Attrill, Helen
Antonazzo, Giulia
Thurmond, Jim
Chen, Weihang
Li, Fangge
Chao, Tiffany
Mohr, Stephanie E
Brown, Nicholas H
Perrimon, Norbert
author_facet Hu, Yanhui
Comjean, Aram
Attrill, Helen
Antonazzo, Giulia
Thurmond, Jim
Chen, Weihang
Li, Fangge
Chao, Tiffany
Mohr, Stephanie E
Brown, Nicholas H
Perrimon, Norbert
author_sort Hu, Yanhui
collection PubMed
description Gene set enrichment analysis (GSEA) plays an important role in large-scale data analysis, helping scientists discover the underlying biological patterns over-represented in a gene list resulting from, for example, an ‘omics’ study. Gene Ontology (GO) annotation is the most frequently used classification mechanism for gene set definition. Here we present a new GSEA tool, PANGEA (PAthway, Network and Gene-set Enrichment Analysis; https://www.flyrnai.org/tools/pangea/), developed to allow a more flexible and configurable approach to data analysis using a variety of classification sets. PANGEA allows GO analysis to be performed on different sets of GO annotations, for example excluding high-throughput studies. Beyond GO, gene sets for pathway annotation and protein complex data from various resources as well as expression and disease annotation from the Alliance of Genome Resources (Alliance). In addition, visualizations of results are enhanced by providing an option to view network of gene set to gene relationships. The tool also allows comparison of multiple input gene lists and accompanying visualisation tools for quick and easy comparison. This new tool will facilitate GSEA for Drosophila and other major model organisms based on high-quality annotated information available for these species.
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spelling pubmed-103200582023-07-06 PANGEA: a new gene set enrichment tool for Drosophila and common research organisms Hu, Yanhui Comjean, Aram Attrill, Helen Antonazzo, Giulia Thurmond, Jim Chen, Weihang Li, Fangge Chao, Tiffany Mohr, Stephanie E Brown, Nicholas H Perrimon, Norbert Nucleic Acids Res Web Server Issue Gene set enrichment analysis (GSEA) plays an important role in large-scale data analysis, helping scientists discover the underlying biological patterns over-represented in a gene list resulting from, for example, an ‘omics’ study. Gene Ontology (GO) annotation is the most frequently used classification mechanism for gene set definition. Here we present a new GSEA tool, PANGEA (PAthway, Network and Gene-set Enrichment Analysis; https://www.flyrnai.org/tools/pangea/), developed to allow a more flexible and configurable approach to data analysis using a variety of classification sets. PANGEA allows GO analysis to be performed on different sets of GO annotations, for example excluding high-throughput studies. Beyond GO, gene sets for pathway annotation and protein complex data from various resources as well as expression and disease annotation from the Alliance of Genome Resources (Alliance). In addition, visualizations of results are enhanced by providing an option to view network of gene set to gene relationships. The tool also allows comparison of multiple input gene lists and accompanying visualisation tools for quick and easy comparison. This new tool will facilitate GSEA for Drosophila and other major model organisms based on high-quality annotated information available for these species. Oxford University Press 2023-05-01 /pmc/articles/PMC10320058/ /pubmed/37125646 http://dx.doi.org/10.1093/nar/gkad331 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Web Server Issue
Hu, Yanhui
Comjean, Aram
Attrill, Helen
Antonazzo, Giulia
Thurmond, Jim
Chen, Weihang
Li, Fangge
Chao, Tiffany
Mohr, Stephanie E
Brown, Nicholas H
Perrimon, Norbert
PANGEA: a new gene set enrichment tool for Drosophila and common research organisms
title PANGEA: a new gene set enrichment tool for Drosophila and common research organisms
title_full PANGEA: a new gene set enrichment tool for Drosophila and common research organisms
title_fullStr PANGEA: a new gene set enrichment tool for Drosophila and common research organisms
title_full_unstemmed PANGEA: a new gene set enrichment tool for Drosophila and common research organisms
title_short PANGEA: a new gene set enrichment tool for Drosophila and common research organisms
title_sort pangea: a new gene set enrichment tool for drosophila and common research organisms
topic Web Server Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10320058/
https://www.ncbi.nlm.nih.gov/pubmed/37125646
http://dx.doi.org/10.1093/nar/gkad331
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