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GenePlexus: a web-server for gene discovery using network-based machine learning

Biomedical researchers take advantage of high-throughput, high-coverage technologies to routinely generate sets of genes of interest across a wide range of biological conditions. Although these technologies have directly shed light on the molecular underpinnings of various biological processes and d...

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Autores principales: Mancuso, Christopher A, Bills, Patrick S, Krum, Douglas, Newsted, Jacob, Liu, Renming, Krishnan, Arjun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9252732/
https://www.ncbi.nlm.nih.gov/pubmed/35580053
http://dx.doi.org/10.1093/nar/gkac335
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author Mancuso, Christopher A
Bills, Patrick S
Krum, Douglas
Newsted, Jacob
Liu, Renming
Krishnan, Arjun
author_facet Mancuso, Christopher A
Bills, Patrick S
Krum, Douglas
Newsted, Jacob
Liu, Renming
Krishnan, Arjun
author_sort Mancuso, Christopher A
collection PubMed
description Biomedical researchers take advantage of high-throughput, high-coverage technologies to routinely generate sets of genes of interest across a wide range of biological conditions. Although these technologies have directly shed light on the molecular underpinnings of various biological processes and diseases, the list of genes from any individual experiment is often noisy and incomplete. Additionally, interpreting these lists of genes can be challenging in terms of how they are related to each other and to other genes in the genome. In this work, we present GenePlexus (https://www.geneplexus.net/), a web-server that allows a researcher to utilize a powerful, network-based machine learning method to gain insights into their gene set of interest and additional functionally similar genes. Once a user uploads their own set of human genes and chooses between a number of different human network representations, GenePlexus provides predictions of how associated every gene in the network is to the input set. The web-server also provides interpretability through network visualization and comparison to other machine learning models trained on thousands of known process/pathway and disease gene sets. GenePlexus is free and open to all users without the need for registration.
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spelling pubmed-92527322022-07-05 GenePlexus: a web-server for gene discovery using network-based machine learning Mancuso, Christopher A Bills, Patrick S Krum, Douglas Newsted, Jacob Liu, Renming Krishnan, Arjun Nucleic Acids Res Web Server Issue Biomedical researchers take advantage of high-throughput, high-coverage technologies to routinely generate sets of genes of interest across a wide range of biological conditions. Although these technologies have directly shed light on the molecular underpinnings of various biological processes and diseases, the list of genes from any individual experiment is often noisy and incomplete. Additionally, interpreting these lists of genes can be challenging in terms of how they are related to each other and to other genes in the genome. In this work, we present GenePlexus (https://www.geneplexus.net/), a web-server that allows a researcher to utilize a powerful, network-based machine learning method to gain insights into their gene set of interest and additional functionally similar genes. Once a user uploads their own set of human genes and chooses between a number of different human network representations, GenePlexus provides predictions of how associated every gene in the network is to the input set. The web-server also provides interpretability through network visualization and comparison to other machine learning models trained on thousands of known process/pathway and disease gene sets. GenePlexus is free and open to all users without the need for registration. Oxford University Press 2022-05-17 /pmc/articles/PMC9252732/ /pubmed/35580053 http://dx.doi.org/10.1093/nar/gkac335 Text en © The Author(s) 2022. 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
Mancuso, Christopher A
Bills, Patrick S
Krum, Douglas
Newsted, Jacob
Liu, Renming
Krishnan, Arjun
GenePlexus: a web-server for gene discovery using network-based machine learning
title GenePlexus: a web-server for gene discovery using network-based machine learning
title_full GenePlexus: a web-server for gene discovery using network-based machine learning
title_fullStr GenePlexus: a web-server for gene discovery using network-based machine learning
title_full_unstemmed GenePlexus: a web-server for gene discovery using network-based machine learning
title_short GenePlexus: a web-server for gene discovery using network-based machine learning
title_sort geneplexus: a web-server for gene discovery using network-based machine learning
topic Web Server Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9252732/
https://www.ncbi.nlm.nih.gov/pubmed/35580053
http://dx.doi.org/10.1093/nar/gkac335
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