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Arabidopsis Transcription Regulatory Factor Domain/Domain Interaction Analysis Tool—Liquid/Liquid Phase Separation, Oligomerization, GO Analysis: A Toolkit for Interaction Data-Based Domain Analysis

Although a large number of databases are available for regulatory elements, a bottleneck has been created by the lack of bioinformatics tools to predict the interaction modes of regulatory elements. To reduce this gap, we developed the Arabidopsis Transcription Regulatory Factor Domain/Domain Intera...

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Autores principales: Kang, Jee Eun, Jun, Ji Hae, Kwon, Jung Hyun, Lee, Ju-Hyun, Hwang, Kidong, Kim, Sungjong, Jeong, Namhee
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10379056/
https://www.ncbi.nlm.nih.gov/pubmed/37510380
http://dx.doi.org/10.3390/genes14071476
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author Kang, Jee Eun
Jun, Ji Hae
Kwon, Jung Hyun
Lee, Ju-Hyun
Hwang, Kidong
Kim, Sungjong
Jeong, Namhee
author_facet Kang, Jee Eun
Jun, Ji Hae
Kwon, Jung Hyun
Lee, Ju-Hyun
Hwang, Kidong
Kim, Sungjong
Jeong, Namhee
author_sort Kang, Jee Eun
collection PubMed
description Although a large number of databases are available for regulatory elements, a bottleneck has been created by the lack of bioinformatics tools to predict the interaction modes of regulatory elements. To reduce this gap, we developed the Arabidopsis Transcription Regulatory Factor Domain/Domain Interaction Analysis Tool–liquid/liquid phase separation (LLPS), oligomerization, GO analysis (ART FOUNDATION-LOG), a useful toolkit for protein–nucleic acid interaction (PNI) and protein–protein interaction (PPI) analysis based on domain–domain interactions (DDIs). LLPS, protein oligomerization, the structural properties of protein domains, and protein modifications are major components in the orchestration of the spatiotemporal dynamics of PPIs and PNIs. Our goal is to integrate PPI/PNI information into the development of a prediction model for identifying important genetic variants in peaches. Our program unified interdatabase relational keys based on protein domains to facilitate inference from the model species. A key advantage of this program lies in the integrated information of related features, such as protein oligomerization, LOG analysis, structural characterizations of domains (e.g., domain linkers, intrinsically disordered regions, DDIs, domain–motif (peptide) interactions, beta sheets, and transmembrane helices), and post-translational modification. We provided simple tests to demonstrate how to use this program, which can be applied to other eukaryotic organisms.
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spelling pubmed-103790562023-07-29 Arabidopsis Transcription Regulatory Factor Domain/Domain Interaction Analysis Tool—Liquid/Liquid Phase Separation, Oligomerization, GO Analysis: A Toolkit for Interaction Data-Based Domain Analysis Kang, Jee Eun Jun, Ji Hae Kwon, Jung Hyun Lee, Ju-Hyun Hwang, Kidong Kim, Sungjong Jeong, Namhee Genes (Basel) Article Although a large number of databases are available for regulatory elements, a bottleneck has been created by the lack of bioinformatics tools to predict the interaction modes of regulatory elements. To reduce this gap, we developed the Arabidopsis Transcription Regulatory Factor Domain/Domain Interaction Analysis Tool–liquid/liquid phase separation (LLPS), oligomerization, GO analysis (ART FOUNDATION-LOG), a useful toolkit for protein–nucleic acid interaction (PNI) and protein–protein interaction (PPI) analysis based on domain–domain interactions (DDIs). LLPS, protein oligomerization, the structural properties of protein domains, and protein modifications are major components in the orchestration of the spatiotemporal dynamics of PPIs and PNIs. Our goal is to integrate PPI/PNI information into the development of a prediction model for identifying important genetic variants in peaches. Our program unified interdatabase relational keys based on protein domains to facilitate inference from the model species. A key advantage of this program lies in the integrated information of related features, such as protein oligomerization, LOG analysis, structural characterizations of domains (e.g., domain linkers, intrinsically disordered regions, DDIs, domain–motif (peptide) interactions, beta sheets, and transmembrane helices), and post-translational modification. We provided simple tests to demonstrate how to use this program, which can be applied to other eukaryotic organisms. MDPI 2023-07-19 /pmc/articles/PMC10379056/ /pubmed/37510380 http://dx.doi.org/10.3390/genes14071476 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Kang, Jee Eun
Jun, Ji Hae
Kwon, Jung Hyun
Lee, Ju-Hyun
Hwang, Kidong
Kim, Sungjong
Jeong, Namhee
Arabidopsis Transcription Regulatory Factor Domain/Domain Interaction Analysis Tool—Liquid/Liquid Phase Separation, Oligomerization, GO Analysis: A Toolkit for Interaction Data-Based Domain Analysis
title Arabidopsis Transcription Regulatory Factor Domain/Domain Interaction Analysis Tool—Liquid/Liquid Phase Separation, Oligomerization, GO Analysis: A Toolkit for Interaction Data-Based Domain Analysis
title_full Arabidopsis Transcription Regulatory Factor Domain/Domain Interaction Analysis Tool—Liquid/Liquid Phase Separation, Oligomerization, GO Analysis: A Toolkit for Interaction Data-Based Domain Analysis
title_fullStr Arabidopsis Transcription Regulatory Factor Domain/Domain Interaction Analysis Tool—Liquid/Liquid Phase Separation, Oligomerization, GO Analysis: A Toolkit for Interaction Data-Based Domain Analysis
title_full_unstemmed Arabidopsis Transcription Regulatory Factor Domain/Domain Interaction Analysis Tool—Liquid/Liquid Phase Separation, Oligomerization, GO Analysis: A Toolkit for Interaction Data-Based Domain Analysis
title_short Arabidopsis Transcription Regulatory Factor Domain/Domain Interaction Analysis Tool—Liquid/Liquid Phase Separation, Oligomerization, GO Analysis: A Toolkit for Interaction Data-Based Domain Analysis
title_sort arabidopsis transcription regulatory factor domain/domain interaction analysis tool—liquid/liquid phase separation, oligomerization, go analysis: a toolkit for interaction data-based domain analysis
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10379056/
https://www.ncbi.nlm.nih.gov/pubmed/37510380
http://dx.doi.org/10.3390/genes14071476
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