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gsGator: an integrated web platform for cross-species gene set analysis

BACKGROUND: Gene set analysis (GSA) is useful in deducing biological significance of gene lists using a priori defined gene sets such as gene ontology (GO) or pathways. Phenotypic annotation is sparse for human genes, but is far more abundant for other model organisms such as mouse, fly, and worm. O...

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Autores principales: Kang, Hyunjung, Choi, Ikjung, Cho, Sooyoung, Ryu, Daeun, Lee, Sanghyuk, Kim, Wankyu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3898093/
https://www.ncbi.nlm.nih.gov/pubmed/24423189
http://dx.doi.org/10.1186/1471-2105-15-13
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author Kang, Hyunjung
Choi, Ikjung
Cho, Sooyoung
Ryu, Daeun
Lee, Sanghyuk
Kim, Wankyu
author_facet Kang, Hyunjung
Choi, Ikjung
Cho, Sooyoung
Ryu, Daeun
Lee, Sanghyuk
Kim, Wankyu
author_sort Kang, Hyunjung
collection PubMed
description BACKGROUND: Gene set analysis (GSA) is useful in deducing biological significance of gene lists using a priori defined gene sets such as gene ontology (GO) or pathways. Phenotypic annotation is sparse for human genes, but is far more abundant for other model organisms such as mouse, fly, and worm. Often, GSA needs to be done highly interactively by combining or modifying gene lists or inspecting gene-gene interactions in a molecular network. DESCRIPTION: We developed gsGator, a web-based platform for functional interpretation of gene sets with useful features such as cross-species GSA, simultaneous analysis of multiple gene sets, and a fully integrated network viewer for visualizing both GSA results and molecular networks. An extensive set of gene annotation information is amassed including GO & pathways, genomic annotations, protein-protein interaction, transcription factor-target (TF-target), miRNA targeting, and phenotype information for various model organisms. By combining the functionalities of Set Creator, Set Operator and Network Navigator, user can perform highly flexible and interactive GSA by creating a new gene list by any combination of existing gene sets (intersection, union and difference) or expanding genes interactively along the molecular networks such as protein-protein interaction and TF-target. We also demonstrate the utility of our interactive and cross-species GSA implemented in gsGator by several usage examples for interpreting genome-wide association study (GWAS) results. gsGator is freely available at http://gsGator.ewha.ac.kr. CONCLUSIONS: Interactive and cross-species GSA in gsGator greatly extends the scope and utility of GSA, leading to novel insights via conserved functional gene modules across different species.
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spelling pubmed-38980932014-01-23 gsGator: an integrated web platform for cross-species gene set analysis Kang, Hyunjung Choi, Ikjung Cho, Sooyoung Ryu, Daeun Lee, Sanghyuk Kim, Wankyu BMC Bioinformatics Database BACKGROUND: Gene set analysis (GSA) is useful in deducing biological significance of gene lists using a priori defined gene sets such as gene ontology (GO) or pathways. Phenotypic annotation is sparse for human genes, but is far more abundant for other model organisms such as mouse, fly, and worm. Often, GSA needs to be done highly interactively by combining or modifying gene lists or inspecting gene-gene interactions in a molecular network. DESCRIPTION: We developed gsGator, a web-based platform for functional interpretation of gene sets with useful features such as cross-species GSA, simultaneous analysis of multiple gene sets, and a fully integrated network viewer for visualizing both GSA results and molecular networks. An extensive set of gene annotation information is amassed including GO & pathways, genomic annotations, protein-protein interaction, transcription factor-target (TF-target), miRNA targeting, and phenotype information for various model organisms. By combining the functionalities of Set Creator, Set Operator and Network Navigator, user can perform highly flexible and interactive GSA by creating a new gene list by any combination of existing gene sets (intersection, union and difference) or expanding genes interactively along the molecular networks such as protein-protein interaction and TF-target. We also demonstrate the utility of our interactive and cross-species GSA implemented in gsGator by several usage examples for interpreting genome-wide association study (GWAS) results. gsGator is freely available at http://gsGator.ewha.ac.kr. CONCLUSIONS: Interactive and cross-species GSA in gsGator greatly extends the scope and utility of GSA, leading to novel insights via conserved functional gene modules across different species. BioMed Central 2014-01-14 /pmc/articles/PMC3898093/ /pubmed/24423189 http://dx.doi.org/10.1186/1471-2105-15-13 Text en Copyright © 2014 Kang et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database
Kang, Hyunjung
Choi, Ikjung
Cho, Sooyoung
Ryu, Daeun
Lee, Sanghyuk
Kim, Wankyu
gsGator: an integrated web platform for cross-species gene set analysis
title gsGator: an integrated web platform for cross-species gene set analysis
title_full gsGator: an integrated web platform for cross-species gene set analysis
title_fullStr gsGator: an integrated web platform for cross-species gene set analysis
title_full_unstemmed gsGator: an integrated web platform for cross-species gene set analysis
title_short gsGator: an integrated web platform for cross-species gene set analysis
title_sort gsgator: an integrated web platform for cross-species gene set analysis
topic Database
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3898093/
https://www.ncbi.nlm.nih.gov/pubmed/24423189
http://dx.doi.org/10.1186/1471-2105-15-13
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