evolSOM: An R package for analyzing conservation and displacement of biological variables with self-organizing maps

Autores
Prochetto, Santiago; Reinheimer, Renata; Stegmayer, Georgina
Año de publicación
2024
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Motivation: Unraveling the connection between genes and traits is crucial for solving many biological puzzles. Ribonucleic acid molecules and proteins, derived from these genetic instructions, play crucial roles in shaping cell structures, influencing reactions, and guiding behavior. This fundamental biological principle links genetic makeup to observable traits, but integrating and extracting meaningful relationships from this complex, multimodal data present a significant challenge. Results: We introduce evolSOM, a novel R package that allows exploring and visualizing the conservation or displacement of biological variables, easing the integration of phenotypic and genotypic attributes. It enables the projection of multi-dimensional expression profiles onto interpretable two-dimensional grids, aiding in the identification of conserved or displaced genes/phenotypes across multiple conditions. Variables displaced together suggest membership to the same regulatory network, where the nature of the displacement may hold biological significance. The conservation or displacement of variables is automatically calculated and graphically presented by evolSOM. Its user-friendly interface and visualization capabilities enhance the accessibility of complex network analyses.
Fil: Prochetto, Santiago. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentina
Fil: Reinheimer, Renata. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentina
Fil: Stegmayer, Georgina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Materia
conservation
SOM
phenotype
genes
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/264270
Acceder
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network_name_str CONICET Digital (CONICET)
spelling evolSOM: An R package for analyzing conservation and displacement of biological variables with self-organizing mapsProchetto, SantiagoReinheimer, RenataStegmayer, GeorginaconservationSOMphenotypegeneshttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Motivation: Unraveling the connection between genes and traits is crucial for solving many biological puzzles. Ribonucleic acid molecules and proteins, derived from these genetic instructions, play crucial roles in shaping cell structures, influencing reactions, and guiding behavior. This fundamental biological principle links genetic makeup to observable traits, but integrating and extracting meaningful relationships from this complex, multimodal data present a significant challenge. Results: We introduce evolSOM, a novel R package that allows exploring and visualizing the conservation or displacement of biological variables, easing the integration of phenotypic and genotypic attributes. It enables the projection of multi-dimensional expression profiles onto interpretable two-dimensional grids, aiding in the identification of conserved or displaced genes/phenotypes across multiple conditions. Variables displaced together suggest membership to the same regulatory network, where the nature of the displacement may hold biological significance. The conservation or displacement of variables is automatically calculated and graphically presented by evolSOM. Its user-friendly interface and visualization capabilities enhance the accessibility of complex network analyses.Fil: Prochetto, Santiago. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; ArgentinaFil: Reinheimer, Renata. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; ArgentinaFil: Stegmayer, Georgina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaOxford University Press2024-08info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/264270Prochetto, Santiago; Reinheimer, Renata; Stegmayer, Georgina; evolSOM: An R package for analyzing conservation and displacement of biological variables with self-organizing maps; Oxford University Press; Bioinformatics Advances; 4; 1; 8-2024; 1-52635-0041CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbae124/7739165info:eu-repo/semantics/altIdentifier/doi/10.1093/bioadv/vbae124info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T09:50:00Zoai:ri.conicet.gov.ar:11336/264270instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 09:50:01.001CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv evolSOM: An R package for analyzing conservation and displacement of biological variables with self-organizing maps
title evolSOM: An R package for analyzing conservation and displacement of biological variables with self-organizing maps
spellingShingle evolSOM: An R package for analyzing conservation and displacement of biological variables with self-organizing maps
Prochetto, Santiago
conservation
SOM
phenotype
genes
title_short evolSOM: An R package for analyzing conservation and displacement of biological variables with self-organizing maps
title_full evolSOM: An R package for analyzing conservation and displacement of biological variables with self-organizing maps
title_fullStr evolSOM: An R package for analyzing conservation and displacement of biological variables with self-organizing maps
title_full_unstemmed evolSOM: An R package for analyzing conservation and displacement of biological variables with self-organizing maps
title_sort evolSOM: An R package for analyzing conservation and displacement of biological variables with self-organizing maps
dc.creator.none.fl_str_mv Prochetto, Santiago
Reinheimer, Renata
Stegmayer, Georgina
author Prochetto, Santiago
author_facet Prochetto, Santiago
Reinheimer, Renata
Stegmayer, Georgina
author_role author
author2 Reinheimer, Renata
Stegmayer, Georgina
author2_role author
author
dc.subject.none.fl_str_mv conservation
SOM
phenotype
genes
topic conservation
SOM
phenotype
genes
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Motivation: Unraveling the connection between genes and traits is crucial for solving many biological puzzles. Ribonucleic acid molecules and proteins, derived from these genetic instructions, play crucial roles in shaping cell structures, influencing reactions, and guiding behavior. This fundamental biological principle links genetic makeup to observable traits, but integrating and extracting meaningful relationships from this complex, multimodal data present a significant challenge. Results: We introduce evolSOM, a novel R package that allows exploring and visualizing the conservation or displacement of biological variables, easing the integration of phenotypic and genotypic attributes. It enables the projection of multi-dimensional expression profiles onto interpretable two-dimensional grids, aiding in the identification of conserved or displaced genes/phenotypes across multiple conditions. Variables displaced together suggest membership to the same regulatory network, where the nature of the displacement may hold biological significance. The conservation or displacement of variables is automatically calculated and graphically presented by evolSOM. Its user-friendly interface and visualization capabilities enhance the accessibility of complex network analyses.
Fil: Prochetto, Santiago. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentina
Fil: Reinheimer, Renata. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentina
Fil: Stegmayer, Georgina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
description Motivation: Unraveling the connection between genes and traits is crucial for solving many biological puzzles. Ribonucleic acid molecules and proteins, derived from these genetic instructions, play crucial roles in shaping cell structures, influencing reactions, and guiding behavior. This fundamental biological principle links genetic makeup to observable traits, but integrating and extracting meaningful relationships from this complex, multimodal data present a significant challenge. Results: We introduce evolSOM, a novel R package that allows exploring and visualizing the conservation or displacement of biological variables, easing the integration of phenotypic and genotypic attributes. It enables the projection of multi-dimensional expression profiles onto interpretable two-dimensional grids, aiding in the identification of conserved or displaced genes/phenotypes across multiple conditions. Variables displaced together suggest membership to the same regulatory network, where the nature of the displacement may hold biological significance. The conservation or displacement of variables is automatically calculated and graphically presented by evolSOM. Its user-friendly interface and visualization capabilities enhance the accessibility of complex network analyses.
publishDate 2024
dc.date.none.fl_str_mv 2024-08
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/264270
Prochetto, Santiago; Reinheimer, Renata; Stegmayer, Georgina; evolSOM: An R package for analyzing conservation and displacement of biological variables with self-organizing maps; Oxford University Press; Bioinformatics Advances; 4; 1; 8-2024; 1-5
2635-0041
CONICET Digital
CONICET
url http://hdl.handle.net/11336/264270
identifier_str_mv Prochetto, Santiago; Reinheimer, Renata; Stegmayer, Georgina; evolSOM: An R package for analyzing conservation and displacement of biological variables with self-organizing maps; Oxford University Press; Bioinformatics Advances; 4; 1; 8-2024; 1-5
2635-0041
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbae124/7739165
info:eu-repo/semantics/altIdentifier/doi/10.1093/bioadv/vbae124
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.13397

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