SEBINI-CABIN: An Analysis Pipeline for Biological Network Inference, with a Case Study in Protein-Protein Interaction Network Reconstruction

2007 ◽  
Author(s):  
Ronald C. Taylor ◽  
Jason McDermott ◽  
W. Hayes McDonald ◽  
Dale Pelletier ◽  
Denise Schmoyer ◽  
...  
Keyword(s):  
Protein Interaction ◽  
Protein Interaction Network ◽  
Network Inference ◽  
Biological Network ◽  
Interaction Network ◽  
Network Reconstruction ◽  
Analysis Pipeline ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Network

scholarly journals Network Modules Driving Plant Stress Response, Tolerance and Adaptation: A case study using Abscisic acid Induced Protein-protein Interactome of Arabidopsis thaliana

2016 ◽  
Author(s):  
Khader Shameer ◽  
Mahantesha Naika ◽  
Oommen K. Mathew ◽  
Ramanathan Sowdhamini
Keyword(s):  
Abscisic Acid ◽  
Abiotic Stress ◽  
Protein Interaction ◽  
Biological Network ◽  
Interaction Network ◽  
Detection Algorithm ◽  
Protein Protein Interaction ◽  
Complex Detection ◽  
Protein Protein Interaction Network

AbstractUnderstanding key protein-protein interaction network mediated by genes responsive to biotic and abiotic stress could help to understand the functional modules and network topologies driven genes responsive to stresses. It still remains to be an open question whether distinct protein-protein interaction networks have functional or regulatory role in mediating abiotic or biotic stress response in plants. To address this question we compiled abscisic acid responsive genes from Stress-responsive TranscrIption Factor DataBase (version 2; STIFDB2); derived protein-protein interaction network mediated by the genes from STRING database and performed biological network analyses using Cytoscape plugins. We have used Molecular Complex Detection algorithm for deriving highly connected module from the abscisic acid responsive network. Biological Network Gene Ontology tool was used to derive functional enrichment of abscisic acid responsive interaction network using GOSlim_Plants ontology. GraphletCounter was used to identify graph motifs in the network and NetworkAnalyzer was used to compute various network topological parameters. We found 26S proteasome subunits as a highly clustered module using Molecular Complex Detection algorithm. Enrichment analysis indicates that several biological processes terms including “flower development” are associated with the network. Results from this case study can be used to understand network properties of abiotic stress responsive genes and gene products in a model plant system.

scholarly journals Understanding protein‐protein interaction network: a case study with glutaminase interacting protein

2013 ◽  
Vol 27 (S1) ◽  
Author(s):  
Mohiuddin Ovee ◽  
David Zoetewey ◽  
Monimoy Banerjee ◽  
Rajagopalan Bhaskaran ◽  
Smita Mohanty ◽  
...  
Keyword(s):  
Protein Interaction ◽  
Protein Interaction Network ◽  
Interaction Network ◽  
Interacting Protein ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Network

scholarly journals Diabetic Retinopathy and Laser Therapy in Rats: A Protein-Protein Interaction Network Analysis

2017 ◽  
Vol 8 (Suppl 1) ◽  
pp. S20-S21 ◽  
Author(s):  
Akram Safaei ◽  
Mostafa Rezaei Tavirani ◽  
Mona Zamanian Azodi ◽  
Alireza Lashay ◽  
Seyed Farzad Mohammadi ◽  
...  
Keyword(s):  
Diabetic Retinopathy ◽  
Network Analysis ◽  
Laser Therapy ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
Interaction Network ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Network
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