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

Authors :
Lianhong Ding
Shaoshuai Xie
Shucui Zhang
Hangyu Shen
Huaqiang Zhong
Daoyuan Li
Peng Shi
Lianli Chi
Qunye Zhang
Source :
Frontiers in Molecular Biosciences, Vol 7 (2020)
Publication Year :
2020
Publisher :
Frontiers Media S.A., 2020.

Abstract

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.

Details

Language :
English
ISSN :
2296889X
Volume :
7
Database :
Directory of Open Access Journals
Journal :
Frontiers in Molecular Biosciences
Publication Type :
Academic Journal
Accession number :
edsdoj.7e7331bd4b4445c59e5efea5c3a377ab
Document Type :
article
Full Text :
https://doi.org/10.3389/fmolb.2020.606570