Tag: Interaction Networks

Cytoprophet 1.0 – A Cytoscape plug-in for Protein and Domain Interaction Networks Inference

Cytoprophet 1.0

:: DESCRIPTION

Cytoprophet is a project developed by the Laboratory for Computational Life Sciences at the Computer Science Department of the University of Notre Dame. It is a tool to help researchers to infer new potential protein (PPI) and domain (DDI) interactions. It is implemented as a Cytoscape plugin, where users input a set of proteins and retrieve a network of plausible protein and domain interactions with a score. Three algorithms are used for the estimation of PPI/DDI: Maximum Specificity Set Cover (MSSC) Approach, Maximum Likelihood Estimation (MLE) and the Sum-Product Algorithm (SPA) for protein networks.

::DEVELOPER

Cytoprophet team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Cytoprophet

:: MORE INFORMATION

Citation

Chengbang Huang , Faruck Morcos, Simon P. Kanaan, Stefan Wuchty, Danny Z. Chen, and Jesús A. Izaguirre
Predicting Protein-Protein Interactions from Protein Domains Using a Set Cover Approach.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol 4 pp. 78-87. Jan-March 2007

JRIM – Joint reconstruct cis-regulatory interaction networks of multiple cell populations

JRIM

:: DESCRIPTION

JRIM is a package for Jointly Reconstructing cis-regulatory Interaction Maps of multiple cell populations using single-cell chromatin accessibility data and identifying shared and common interaction patterns. It uses an aggregation process to deal with the sparsity of single-cell data, exploits similarity between cell types via a group lasso penalty, and generates comparable networks. JRIM could be used to characterize difference between cell types or identify dynamic changes during cell development.

::DEVELOPER

Shihua Zhang’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

JRIM

:: MORE INFORMATION

Citation

Dong K, Zhang S.
Joint reconstruction of cis-regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data.
Brief Bioinform. 2021 May 20;22(3):bbaa120. doi: 10.1093/bib/bbaa120. PMID: 32578841; PMCID: PMC8138825.

VirHostNet 2.0 – Knowledgebase for the management and analysis of Proteome Wide Virus-host Interaction Networks

VirHostNet 2.0

:: DESCRIPTION

VirHostNet (Virus-Host Network) is a knowledgebase system dedicated to the curation, the integration, the management and the analysis of virus-host molecular (mainly protein-protein) interaction networks as well as their functional annotation (molecular functions, cellular pathways, protein domains).

::DEVELOPER

VirHostNet team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks.
Navratil V, de Chassey B, Meyniel L, Delmotte S, Gautier C, André P, Lotteau V, Rabourdin-Combe C.
Nucleic Acids Res. 2009 Jan;37(Database issue):D661-8. doi: 10.1093/nar/gkn794.