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Subnetwork extraction software tools | Pathway analysis

The extraction of targeted subnetworks is a powerful way to identify functional modules and pathways within complex networks.

Source text:
(Lemetre et al., 2013) SubNet: a Java application for subnetwork extraction. Bioinformatics.

LANDD
Desktop

LANDD Liquid Association for Network Dynamics Detection

Finds subnetworks that show substantial dynamic correlations. LANDD focuses on…

Finds subnetworks that show substantial dynamic correlations. LANDD focuses on subnetworks that tend to comprise functionally related genes. It uses collective behaviour of genes in a subnetwork,…

PhenomeScape
Desktop

PhenomeScape

Provides easy access to the PhenomeExpress algorithm to interpret gene…

Provides easy access to the PhenomeExpress algorithm to interpret gene expression data. Compared to existing tools, PhenomeScape is unique in allowing integration of the prior phenotypic knowledge of…

LncSubpathway
Web

LncSubpathway

Detects transcriptional subpathway dysregulation that related with dysregulated…

Detects transcriptional subpathway dysregulation that related with dysregulated long non-coding RNAs (lncRNAs). LncSubpathway is a computational method that integrates transcriptional expression,…

ModuleBlast
Desktop
Web

ModuleBlast

Finding an active sub-network is a hard problem and applying it across species…

Finding an active sub-network is a hard problem and applying it across species requires further considerations (e.g. orthology information, expression data and networks from different sources). To…

PCSF
Desktop

PCSF Prize-Collecting Steiner Forest

Performs analysis of high-throughput data using the interaction networks as a…

Performs analysis of high-throughput data using the interaction networks as a template, and interprets the biological landscape of interactome with respect to the data. PCSF allows user to i) upload…

MinePath
Web

MinePath

A pathway analysis methodology. MinePath facilitates the decomposition of…

A pathway analysis methodology. MinePath facilitates the decomposition of pathways into their constituent sub-paths. Decomposition leads to the transformation of single-relations to complex…

EAModules
Desktop

EAModules

Provides an active module identification algorithm based on a memetic method.…

Provides an active module identification algorithm based on a memetic method. EAModules offers a direct strategy on a set of nodes to get connected subnetworks, thus avoid complicated graph divide…

RelExplain
Web

RelExplain

Analyzes a particular biological process bp in the context of a given network…

Analyzes a particular biological process bp in the context of a given network to unravel the relevant relationships of the involved genes in the process. RelExplain is a method designed to find…

samplingPaperSo…
Desktop

samplingPaperSoftware

Assess when a given subnetwork differs significantly from randomly generated…

Assess when a given subnetwork differs significantly from randomly generated subnetworks. samplingPaperSoftware is an alternative null model that is based on an ensemble of seed lists generated from…

Signet
Desktop

Signet Selection Inference in Gene NETworks

Allows to study the human adaptation from a gene network perspective. Signet is…

Allows to study the human adaptation from a gene network perspective. Signet is a package that identifies potential undiscovered targets of selection, like pleiotrophin or neuroligins. This method…

G T A T C G C T A
BioGranat-IG
Desktop

BioGranat-IG BioGranat Individuals-Grouping

A BioGranat plugin for the analysis of exome-sequencing data with the aim of…

A BioGranat plugin for the analysis of exome-sequencing data with the aim of identifying groups of genes in biological networks collectively responsible for causing a disease through genetic…

xHeinz
Desktop
Web

xHeinz

A mathematical model for finding active subnetwork modules that are conserved…

A mathematical model for finding active subnetwork modules that are conserved between two species. These are sets of genes, one for each species, which (i) induce a connected subnetwork in a…

BMRF-Net
Desktop

BMRF-Net

A package implemented in Java and C++ to identify protein interaction…

A package implemented in Java and C++ to identify protein interaction subnetworks based on a bagging Markov random field (BMRF) framework. With its user friendly GUI and concurrency options enabled…

COSINE
Desktop

COSINE COndition SpecIfic sub-Network

Employs a scoring function that jointly measures the condition-specific changes…

Employs a scoring function that jointly measures the condition-specific changes of both 'nodes' (individual genes) and 'edges' (gene-gene co-expression). COSINE uses the genetic…

ChainRank
Desktop

ChainRank

Finds relevant subnetworks by identifying and scoring chains of interactions…

Finds relevant subnetworks by identifying and scoring chains of interactions that link specific network components. Scores can be generated from integrating multiple general and context specific…

ReactomeFIViz
Desktop

ReactomeFIViz

Provides a suite of features to assist biologists in performing pathway- and…

Provides a suite of features to assist biologists in performing pathway- and network-based data analysis in a biologically intuitive and user-friendly way. Biologists can use ReactomeFIViz to uncover…

FunMod
Desktop

FunMod

An innovative Cytoscape version 2.8 plugin that is able to mine undirected…

An innovative Cytoscape version 2.8 plugin that is able to mine undirected protein-protein networks and to infer sub-networks of interacting proteins intimately correlated with relevant biological…

TimeXNet
Desktop

TimeXNet

Detects active gene sub-networks with temporal paths. TimeXNet is a standalone…

Detects active gene sub-networks with temporal paths. TimeXNet is a standalone software which can be run via both a graphic and a command-line interface. The software exploits a large molecular…

WMAXC
Desktop

WMAXC Weighted MAXimum Clique

A method for identifying condition specific sub-network. WMAXC first proposes…

A method for identifying condition specific sub-network. WMAXC first proposes scoring functions that jointly measure condition-specific changes to both individual genes and gene-gene co-expressions.…

PhenomeExpress
Desktop

PhenomeExpress

Allows detection of sub-networks relevant to the disease of interest.…

Allows detection of sub-networks relevant to the disease of interest. PhenomeExpress, utilises both the transciptomics data being analysed and the prior knowledge of all cross-species phenotype to…

MMG
Desktop

MMG Mixture Model on Graphs

Identifies differentially expressed submodules of biological networks and…

Identifies differentially expressed submodules of biological networks and pathways. MMG can easily incorporate information about weights in the network, is robust against missing data and can be…

BioNet
Desktop

BioNet

A comprehensive R-package for the analysis of biological networks including an…

A comprehensive R-package for the analysis of biological networks including an exact and a heuristic approach to identify functional modules. The BioNet package provides an extensive framework for…

GXNA
Desktop

GXNA Gene eXpression Network Analysis

An innovative method for analyzing gene expression data using gene interaction…

An innovative method for analyzing gene expression data using gene interaction networks. The method is implemented in software that is publicly available and can be used on virtually any microarray…

planet LiSA
Desktop

planet LiSA

Provides sophisticated algorithms and data structures for analysing structural…

Provides sophisticated algorithms and data structures for analysing structural information in the life sciences. The applications range from RNA and protein secondary structure alignment over finding…

CySpanningTree
Desktop

CySpanningTree

A Cytoscape app for minimal/maximal spanning tree subnetwork discovery. The…

A Cytoscape app for minimal/maximal spanning tree subnetwork discovery. The subnetwork is extracted as a seperate Cytoscape network. Currently CySpanningTree has Prim's and Kruskal's…

SubNet
Desktop

SubNet

A Java-based stand-alone program for extracting subnetworks, given a basal…

A Java-based stand-alone program for extracting subnetworks, given a basal network and a set of selected nodes. Designed with a graphical user-friendly interface, SubNet combines four different…

GenRev
Desktop

GenRev

A network-based software package developed to explore the functional relevance…

A network-based software package developed to explore the functional relevance of genes generated as an intermediate result from numerous high-throughput technologies. GenRev searches for optimal…

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