Cargando…

Feature importance network reveals novel functional relationships between biological features in Arabidopsis thaliana

Understanding how the different cellular components are working together to form a living cell requires multidisciplinary approaches combining molecular and computational biology. Machine learning shows great potential in life sciences, as it can find novel relationships between biological features....

Descripción completa

Detalles Bibliográficos
Autores principales: Ng, Jonathan Wei Xiong, Chua, Swee Kwang, Mutwil, Marek
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9539877/
https://www.ncbi.nlm.nih.gov/pubmed/36212273
http://dx.doi.org/10.3389/fpls.2022.944992
_version_ 1784803587684040704
author Ng, Jonathan Wei Xiong
Chua, Swee Kwang
Mutwil, Marek
author_facet Ng, Jonathan Wei Xiong
Chua, Swee Kwang
Mutwil, Marek
author_sort Ng, Jonathan Wei Xiong
collection PubMed
description Understanding how the different cellular components are working together to form a living cell requires multidisciplinary approaches combining molecular and computational biology. Machine learning shows great potential in life sciences, as it can find novel relationships between biological features. Here, we constructed a dataset of 11,801 gene features for 31,522 Arabidopsis thaliana genes and developed a machine learning workflow to identify linked features. The detected linked features are visualised as a Feature Important Network (FIN), which can be mined to reveal a variety of novel biological insights pertaining to gene function. We demonstrate how FIN can be used to generate novel insights into gene function. To make this network easily accessible to the scientific community, we present the FINder database, available at finder.plant.tools.
format Online
Article
Text
id pubmed-9539877
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-95398772022-10-08 Feature importance network reveals novel functional relationships between biological features in Arabidopsis thaliana Ng, Jonathan Wei Xiong Chua, Swee Kwang Mutwil, Marek Front Plant Sci Plant Science Understanding how the different cellular components are working together to form a living cell requires multidisciplinary approaches combining molecular and computational biology. Machine learning shows great potential in life sciences, as it can find novel relationships between biological features. Here, we constructed a dataset of 11,801 gene features for 31,522 Arabidopsis thaliana genes and developed a machine learning workflow to identify linked features. The detected linked features are visualised as a Feature Important Network (FIN), which can be mined to reveal a variety of novel biological insights pertaining to gene function. We demonstrate how FIN can be used to generate novel insights into gene function. To make this network easily accessible to the scientific community, we present the FINder database, available at finder.plant.tools. Frontiers Media S.A. 2022-09-23 /pmc/articles/PMC9539877/ /pubmed/36212273 http://dx.doi.org/10.3389/fpls.2022.944992 Text en Copyright © 2022 Ng, Chua and Mutwil. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Ng, Jonathan Wei Xiong
Chua, Swee Kwang
Mutwil, Marek
Feature importance network reveals novel functional relationships between biological features in Arabidopsis thaliana
title Feature importance network reveals novel functional relationships between biological features in Arabidopsis thaliana
title_full Feature importance network reveals novel functional relationships between biological features in Arabidopsis thaliana
title_fullStr Feature importance network reveals novel functional relationships between biological features in Arabidopsis thaliana
title_full_unstemmed Feature importance network reveals novel functional relationships between biological features in Arabidopsis thaliana
title_short Feature importance network reveals novel functional relationships between biological features in Arabidopsis thaliana
title_sort feature importance network reveals novel functional relationships between biological features in arabidopsis thaliana
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9539877/
https://www.ncbi.nlm.nih.gov/pubmed/36212273
http://dx.doi.org/10.3389/fpls.2022.944992
work_keys_str_mv AT ngjonathanweixiong featureimportancenetworkrevealsnovelfunctionalrelationshipsbetweenbiologicalfeaturesinarabidopsisthaliana
AT chuasweekwang featureimportancenetworkrevealsnovelfunctionalrelationshipsbetweenbiologicalfeaturesinarabidopsisthaliana
AT mutwilmarek featureimportancenetworkrevealsnovelfunctionalrelationshipsbetweenbiologicalfeaturesinarabidopsisthaliana