OCSANA is a new software designed to identify and prioritize optimal and minimal combinations of interventions to disrupt the paths between source nodes and target nodes
::DEVELOPER
U900 Institut Curie – INSERM/Mines ParisTech “Bioinformatics and Computational Systems Biology of Cancer
GenCLiP is a literature mining tool that can cluster a list of genes with keywords that are auto-extracted from their up-to-date related literature and then manually curated by the user. GenCLiP can also generate a group of negative control genes and a group of positive control genes for comparing the cluster results with the analyzed genes to filter out un-specific keywords.
The NAIL (Network Analysis and Inference Library) project is a set of tools for solving problems in the life sciences using network (graph) approaches. NAIL includes methods for creating networks, analysing and comparing networks, and for visualising or presenting the results.
SNPrank is an eigenvector centrality algorithm that ranks the importance of single nucleotide polymorphisms (SNPs) in a genetic association interaction network (GAIN). Each SNP is ranked according to its overall contribution to the phenotype, including its main effect and second- and higher-order gene-gene interactions.
iDINGO is an R package to estimate group-specific integrative networks and make inference on the integrative differential networks, considering the biological hierarchy among the platforms
PINBPA (Protein interaction network-based pathway analysis) for genome-wide association studies (GWAS) has been developed as a Cytoscape app, to enable analysis of GWAS data in a network fashion.
NetBox is a Java-based software tool for performing network analysis on human interaction networks. It is pre-loaded with a Human Interaction Network (HIN) derived from four literature curated data sources, including the Human Protein Reference Database (HPRD), Reactome, NCI-Nature Pathway Interaction (PID) Database, and the MSKCC Cancer Cell Map.
Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization.
PINTA is a gene prioritization tool that identifies the most promising candidates within a region when only sparse information about the phenotype is available by replacing this knowledge by experimental data on differential gene expression between affected and healthy individuals. Considering the problem from the perspective of a gene/protein network, it assesses the relevance of a candidate gene by considering the level of differential expression in its network neighborhood under the assumption that strong candidates tend to be surrounded by differentially expressed neighbors.