Groups working on networks and complex systems

Groups working with signaling networks

Biological science links

Aging databases

Chemical compound similarity networks

  • ChemProt: a database of more than 700,000 chemicals, 30,000 proteins and their over 2 million interactions integrated to a human protein-protein interaction network having over 400,000 interactions
  • Connectivity Map similarity of mRNA expression profiles extended with disease mRNA expression profiles
  • iCTNet Cytoscape plug-in, polymorphism (SNP) associations, protein-protein interactions, disease-tissue, tissue-gene and drug-gene relationships: integrated Complex Traits Networks
  • IMID, protein-protein interactions, protein-small molecule interactions, associations of interactions with pathways, species, diseases and Gene Ontology terms with the user-selected integration of manually curated and/or automatically extracted data: integrated molecular interaction database
  • SARANEA: a freely available program to mine structure-activity and structure-selectivity relationship information in compound data sets

Disease related web-resources

  • CIPHER: closeness of unrelated proteins is calculated in the interactome from protein products of disease-related genes, and compared with phenotype similarity profile: large closeness marks a potential new disease-related gene
  • DADA: statistically corrects random walk-based prediction with the degree distribution of the network
  • DisGeNET Cytoscape plug-in:, human disease network
  • Endeavour: integrative method using similarities of neighbors or shortest paths in multiple data sources including interactomes
  • Genes2Networks:, new disease-related genes are predicted by their interactome closeness to known disease-related proteins
  • GPEC Cytoscape plug-in: random walks in the interactome are started from protein products of disease-related genes: frequent visits of a previously unrelated protein mark a potential new disease-related gene
  • iCTNet: a Cytoscape plug-in to construct an integrative network of diseases, associated genes, drugs and tissues (
  • Phenopred: integrative method using similarities of neighbors or shortest paths in multiple data sources including interactomes
  • PRINCIPLE/PRINCE Cytoscape plug-in iterative steps of information flow from disease-related and between interacting proteins: after convergence a large flow of a previously unrelated protein marks potential new disease-related gene
  • Prioritizer:, constructs an integrative network and predicts candidate genes by their network closeness to known disease-related genes
  • rcNet: calculates rank coherences between the integrated network characteristic to the target disease and unrelated diseases
  • VAVIEN: calculates neighborhood similarity in the interactome and prioritizes candidate genes

Drug-target related resources

Gene databases, List of E. coli gene database resources

Genetic networks

Protein databases

Protein structure tools and networks

Protein networks

Text search engines for extracting information on bionetwork

Datamining sites for network buildings

Chemical reactions, metabolic networks

Signaling pathway analyzer tools

Complex system evolution

Network analysis

Network comparison methods

Network datasets

Network visualization

Other mathematical tools

Published by the LINK-Group | Editor: Péter Csermely | Last updated on 10 09 2013
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