GraMoFoNe: a Cytoscape Plugin for Querying Motifs without Topology in Protein-Protein Interactions Networks
نویسندگان
چکیده
During the last decade, data on Protein-Protein Interactions (PPI) has increased in a huge manner. Searching for motifs in PPI Network has thus became a crucial problem to interpret this data. A large part of the literature is devoted to the query of motifs with a given topology. However, the biological data are, by now, so noisy (missing and erroneous information) that the topology of a motif can be unrelevant. Consequently, Lacroix et al. [19] defined a new problem, called GRAPH MOTIF, which consists in searching a multiset of colors in a vertex-colored graph. In this article, we present GraMoFoNe, a plugin to Cytoscape based on a Linear PseudoBoolean optimization solver which handles GRAPH MOTIF and some of its extensions.
منابع مشابه
CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks
SUMMARY Network motifs in integrated molecular networks represent functional relationships between distinct data types. They aggregate to form dense topological structures corresponding to functional modules which cannot be detected by traditional graph clustering algorithms. We developed CyClus3D, a Cytoscape plugin for clustering composite three-node network motifs using a 3D spectral cluster...
متن کاملDecomposing protein networks into domain-domain interactions
UNLABELLED The application of novel experimental techniques has generated large networks of protein-protein interactions. Frequently, important information on the structure and cellular function of protein-protein interactions can be gained from the domains of interacting proteins. We have designed a Cytoscape plugin that decomposes interacting proteins into their respective domains and compute...
متن کاملJEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks
SUMMARY JEPETTO (Java Enrichment of Pathways Extended To TOpology) is a Cytoscape 3.x plugin performing integrative human gene set analysis. It identifies functional associations between genes and known cellular pathways, and processes using protein interaction networks and topological analysis. The plugin integrates information from three separate web servers we published previously, specializ...
متن کاملMapping of TP53 protein network using cytoscape software
TP53 acts as a tumor suppressor in cancer. It induces cell cycle arrest or apoptosis in response to cellular stress and damage. p53 gene alteration could cause uncontrolled cell proliferation.In the present study, we used TP53 gene as the seed in the construction of a protein-protein functional association network to identify genes that might involve in tumorgenesis process with TP53. TP53 prot...
متن کاملEvidence mining and novelty assessment of protein–protein interactions with the ConsensusPathDB plugin for Cytoscape
SUMMARY Protein-protein interaction detection methods are applied on a daily basis by molecular biologists worldwide. After generating a set of potential interactions, biologists face the problem of highlighting the ones that are novel and collecting evidence with respect to literature and annotation. This task can be as tedious as searching for every predicted interaction in several interactio...
متن کامل