scholarly journals A computational framework for distinguishing directversusindirect interactions in human functional protein–protein interaction networks

2017 ◽  
Vol 9 (7) ◽  
pp. 595-606 ◽  
Author(s):  
Suyu Mei ◽  
Erik K. Flemington ◽  
Kun Zhang
Keyword(s):  
Protein Interaction ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Functional Protein ◽  
Computational Framework ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Networks

scholarly journals ANAT 3.0: a framework for elucidating functional protein subnetworks using graph-theoretic and machine learning approaches

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
L. F. Signorini ◽  
T. Almozlino ◽  
R. Sharan
Keyword(s):  
Machine Learning ◽  
Protein Interaction ◽  
Network Reconstruction ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Reconstruction Algorithms ◽  
Functional Protein ◽  
Protein Protein Interaction ◽  
Graphical Tool ◽  
Protein Protein Interaction Networks

Abstract Background ANAT is a Cytoscape plugin for the inference of functional protein–protein interaction networks in yeast and human. It is a flexible graphical tool for scientists to explore and elucidate the protein–protein interaction pathways of a process under study. Results Here we present ANAT3.0, which comes with updated PPI network databases of 544,455 (human) and 155,504 (yeast) interactions, and a new machine-learning layer for refined network elucidation. Together they improve network reconstruction to more than twofold increase in the quality of reconstructing known signaling pathways from KEGG. Conclusions ANAT3.0 includes improved network reconstruction algorithms and more comprehensive protein–protein interaction networks than previous versions. ANAT is available for download on the Cytoscape Appstore and at https://www.cs.tau.ac.il/~bnet/ANAT/.

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