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Delayed Comparison and Apriori Algorithm (DCAA): A Tool for Discovering Protein–Protein Interactions From Time-Series Phosphoproteomic Data

Analysis of high-throughput omics data is one of the most important approaches for obtaining information regarding interactions between proteins/genes. Time-series omics data are a series of omics data points indexed in time order and normally contain more abundant information about the interactions...

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Autores principales: Ding, Lianhong, Xie, Shaoshuai, Zhang, Shucui, Shen, Hangyu, Zhong, Huaqiang, Li, Daoyuan, Shi, Peng, Chi, Lianli, Zhang, Qunye
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7758479/
https://www.ncbi.nlm.nih.gov/pubmed/33363212
http://dx.doi.org/10.3389/fmolb.2020.606570
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author Ding, Lianhong
Xie, Shaoshuai
Zhang, Shucui
Shen, Hangyu
Zhong, Huaqiang
Li, Daoyuan
Shi, Peng
Chi, Lianli
Zhang, Qunye
author_facet Ding, Lianhong
Xie, Shaoshuai
Zhang, Shucui
Shen, Hangyu
Zhong, Huaqiang
Li, Daoyuan
Shi, Peng
Chi, Lianli
Zhang, Qunye
author_sort Ding, Lianhong
collection PubMed
description Analysis of high-throughput omics data is one of the most important approaches for obtaining information regarding interactions between proteins/genes. Time-series omics data are a series of omics data points indexed in time order and normally contain more abundant information about the interactions between biological macromolecules than static omics data. In addition, phosphorylation is a key posttranslational modification (PTM) that is indicative of possible protein function changes in cellular processes. Analysis of time-series phosphoproteomic data should provide more meaningful information about protein interactions. However, although many algorithms, databases, and websites have been developed to analyze omics data, the tools dedicated to discovering molecular interactions from time-series omics data, especially from time-series phosphoproteomic data, are still scarce. Moreover, most reported tools ignore the lag between functional alterations and the corresponding changes in protein synthesis/PTM and are highly dependent on previous knowledge, resulting in high false-positive rates and difficulties in finding newly discovered protein–protein interactions (PPIs). Therefore, in the present study, we developed a new method to discover protein–protein interactions with the delayed comparison and Apriori algorithm (DCAA) to address the aforementioned problems. DCAA is based on the idea that there is a lag between functional alterations and the corresponding changes in protein synthesis/PTM. The Apriori algorithm was used to mine association rules from the relationships between items in a dataset and find PPIs based on time-series phosphoproteomic data. The advantage of DCAA is that it does not rely on previous knowledge and the PPI database. The analysis of actual time-series phosphoproteomic data showed that more than 68% of the protein interactions/regulatory relationships predicted by DCAA were accurate. As an analytical tool for PPIs that does not rely on a priori knowledge, DCAA should be useful to predict PPIs from time-series omics data, and this approach is not limited to phosphoproteomic data.
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spelling pubmed-77584792020-12-25 Delayed Comparison and Apriori Algorithm (DCAA): A Tool for Discovering Protein–Protein Interactions From Time-Series Phosphoproteomic Data Ding, Lianhong Xie, Shaoshuai Zhang, Shucui Shen, Hangyu Zhong, Huaqiang Li, Daoyuan Shi, Peng Chi, Lianli Zhang, Qunye Front Mol Biosci Molecular Biosciences Analysis of high-throughput omics data is one of the most important approaches for obtaining information regarding interactions between proteins/genes. Time-series omics data are a series of omics data points indexed in time order and normally contain more abundant information about the interactions between biological macromolecules than static omics data. In addition, phosphorylation is a key posttranslational modification (PTM) that is indicative of possible protein function changes in cellular processes. Analysis of time-series phosphoproteomic data should provide more meaningful information about protein interactions. However, although many algorithms, databases, and websites have been developed to analyze omics data, the tools dedicated to discovering molecular interactions from time-series omics data, especially from time-series phosphoproteomic data, are still scarce. Moreover, most reported tools ignore the lag between functional alterations and the corresponding changes in protein synthesis/PTM and are highly dependent on previous knowledge, resulting in high false-positive rates and difficulties in finding newly discovered protein–protein interactions (PPIs). Therefore, in the present study, we developed a new method to discover protein–protein interactions with the delayed comparison and Apriori algorithm (DCAA) to address the aforementioned problems. DCAA is based on the idea that there is a lag between functional alterations and the corresponding changes in protein synthesis/PTM. The Apriori algorithm was used to mine association rules from the relationships between items in a dataset and find PPIs based on time-series phosphoproteomic data. The advantage of DCAA is that it does not rely on previous knowledge and the PPI database. The analysis of actual time-series phosphoproteomic data showed that more than 68% of the protein interactions/regulatory relationships predicted by DCAA were accurate. As an analytical tool for PPIs that does not rely on a priori knowledge, DCAA should be useful to predict PPIs from time-series omics data, and this approach is not limited to phosphoproteomic data. Frontiers Media S.A. 2020-12-10 /pmc/articles/PMC7758479/ /pubmed/33363212 http://dx.doi.org/10.3389/fmolb.2020.606570 Text en Copyright © 2020 Ding, Xie, Zhang, Shen, Zhong, Li, Shi, Chi and Zhang. http://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 Molecular Biosciences
Ding, Lianhong
Xie, Shaoshuai
Zhang, Shucui
Shen, Hangyu
Zhong, Huaqiang
Li, Daoyuan
Shi, Peng
Chi, Lianli
Zhang, Qunye
Delayed Comparison and Apriori Algorithm (DCAA): A Tool for Discovering Protein–Protein Interactions From Time-Series Phosphoproteomic Data
title Delayed Comparison and Apriori Algorithm (DCAA): A Tool for Discovering Protein–Protein Interactions From Time-Series Phosphoproteomic Data
title_full Delayed Comparison and Apriori Algorithm (DCAA): A Tool for Discovering Protein–Protein Interactions From Time-Series Phosphoproteomic Data
title_fullStr Delayed Comparison and Apriori Algorithm (DCAA): A Tool for Discovering Protein–Protein Interactions From Time-Series Phosphoproteomic Data
title_full_unstemmed Delayed Comparison and Apriori Algorithm (DCAA): A Tool for Discovering Protein–Protein Interactions From Time-Series Phosphoproteomic Data
title_short Delayed Comparison and Apriori Algorithm (DCAA): A Tool for Discovering Protein–Protein Interactions From Time-Series Phosphoproteomic Data
title_sort delayed comparison and apriori algorithm (dcaa): a tool for discovering protein–protein interactions from time-series phosphoproteomic data
topic Molecular Biosciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7758479/
https://www.ncbi.nlm.nih.gov/pubmed/33363212
http://dx.doi.org/10.3389/fmolb.2020.606570
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