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Topology-based pathway analysis software tools | Gene expression

The goal of pathway analysis is to identify the pathways significantly impacted in a given phenotype. Many current methods are based on algorithms that consider pathways as simple gene lists, dramatically under-utilizing the knowledge that such…
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DAVID
Web

DAVID Database for Annotation, Visualization and Integrated Discovery

A web-based online bioinformatics resource that aims to provide tools for the…

A web-based online bioinformatics resource that aims to provide tools for the functional interpretation of large lists of genes/proteins. DAVID has been used by researchers from more than 5000…

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Ontologizer
Desktop

Ontologizer

A Java application that can be used to perform statistical analysis for…

A Java application that can be used to perform statistical analysis for overrepresentation of Gene Ontology (GO) terms in sets of genes or proteins derived from an experiment. The Ontologizer…

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Pathway-Express
Web

Pathway-Express

Helps the researchers to better understand the biological phenomenon under…

Helps the researchers to better understand the biological phenomenon under study. Pathway-Express permits point out statistically significant cellular functions. It provides a method that…

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WebGestalt
Web

WebGestalt WEB-based GEne SeT AnaLysis Toolkit

Permits the management, information retrieval, organization, visualization and…

Permits the management, information retrieval, organization, visualization and statistical analysis of large sets of genes. WebGestalt integrates functional enrichment analysis and information…

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GeneCodis
Web

GeneCodis

A web-based tool for the ontological analysis of large lists of genes. It can…

A web-based tool for the ontological analysis of large lists of genes. It can be used to determine biological annotations or combinations of annotations that are significantly associated to a list of…

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BrainCell
Desktop

BrainCell

Provides functions to test query gene sets in the context of brain and…

Provides functions to test query gene sets in the context of brain and neurodevelopment. BrainCell contains two databases: BrainH represents gene sets expression pattern across brain regions during…

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EnrichmentBrows…
Desktop

EnrichmentBrowser

Offers a pragmatic solution by enabling the execution and combination of…

Offers a pragmatic solution by enabling the execution and combination of several major set- and network-based enrichment methods. EnrichmentBrowser is an R package that performs three essential…

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NET-GE
Web

NET-GE NETwork-based Gene Enrichment

A web server for associating biological processes and pathways to sets of human…

A web server for associating biological processes and pathways to sets of human proteins involved in the same phenotype. NET-GE is based on protein–protein interaction networks, following the…

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GANPA
Desktop

GANPA Gene Association Network-based Pathway Analysis

Implements a network-based gene weighting algorithm for pathways, as well as a…

Implements a network-based gene weighting algorithm for pathways, as well as a gene-weighted gene set analysis approach for microarray data pathway analysis. As a network-based gene-weighting method,…

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CHRONOS
Desktop

CHRONOS

Detects significantly enriched miRNA mediated subpathways per time point from…

Detects significantly enriched miRNA mediated subpathways per time point from paired miRNA/mRNA time series expression profiles. CHRONOS outperforms current subpathway-based methods into unraveling…

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NetGSA
Desktop

NetGSA Network-based Gene Set Analysis

A constrained network estimation framework that combines network estimation…

A constrained network estimation framework that combines network estimation based on cell- and condition-specific high-dimensional omics data with interaction information from existing data bases.…

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TPEA
Desktop

TPEA Topology-based Pathway Enrichment Analysis

Performs pathway enrichment analysis. TPEA evaluates the importance of nodes…

Performs pathway enrichment analysis. TPEA evaluates the importance of nodes based on their global upstream/downstream positions and the degrees in pathways. It was tested on six gene expression…

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GRAPE
Desktop

GRAPE Gene-Ranking Analysis of Pathway Expression

Allows users to infer whether a pathway is differentially regulated based on…

Allows users to infer whether a pathway is differentially regulated based on the rankings of the genes. GRAPE uses pairwise gene expression ordering within individual samples of a particular…

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PerPAS
Desktop

PerPAS Personalized Pathway Alteration analysiS

Represents a pathway analysis method. PerPAS uses pathway topology information…

Represents a pathway analysis method. PerPAS uses pathway topology information to quantify contribution of an aberrantly expressed gene to pathways and further to characterize pathway activity. The…

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FunNet
Web
Desktop

FunNet

Allows to improve the biological relevance of modular interaction patterns…

Allows to improve the biological relevance of modular interaction patterns found in transcriptional co-expression networks. FunNet was used to explore the transcriptomic signature of the adipose…

Subpathway-GM
Web
Desktop

Subpathway-GM

A powerful analytical method for the identification of biologically meaningful…

A powerful analytical method for the identification of biologically meaningful metabolic subpathways. Subpathway-GM integrates ‘interesting genes’ and ‘interesting metabolites’ related to the…

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PathwayExplorer
Web
Desktop

PathwayExplorer

Provides comprehensive and facile mapping of gene or protein expression…

Provides comprehensive and facile mapping of gene or protein expression profiles. The profiles are simultaneously mapped onto the major regulatory, metabolic and cellular pathways available from the…

SubpathwayMiner
Desktop
Web

SubpathwayMiner

An R-based software package for flexible pathway identification.…

An R-based software package for flexible pathway identification. SubpathwayMiner facilitates sub-pathway identification of metabolic pathways by using pathway structure information. Additionally,…

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PI
Web

PI Pathway Inspector

Finds patterns of expression in complex RNAseq experiments. PI combines two…

Finds patterns of expression in complex RNAseq experiments. PI combines two standard approaches for RNAseq analysis: the identification of differentially expressed genes and a topology-based analysis…

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ToPASeq
Desktop

ToPASeq

Provides a set of easy-to-use and general tools for topology-based pathway…

Provides a set of easy-to-use and general tools for topology-based pathway analysis within the R workspace. ToPASeq offers seven distinct topology-based pathway analysis methods that cover wide range…

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ADGO
Web

ADGO

Provides composite interpretations for microarray data comparing two sample…

Provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. Some other tools also incorporate…

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ChIP-Enrich
Desktop
Web

ChIP-Enrich

Tests ChIP-seq peak data for enrichment of biological pathways, Gene Ontology…

Tests ChIP-seq peak data for enrichment of biological pathways, Gene Ontology terms, and other types of gene sets. Using an input .BED file, ChIP-Enrich assigns peaks to genes based on a chosen…

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GeEtAl2017
Desktop

GeEtAl2017

Offers a method for gene enrichment analysis. The algorithm, based on Fmeasure…

Offers a method for gene enrichment analysis. The algorithm, based on Fmeasure optimization, takes into account precision and recall and provides a flexible threshold for datasets. This approach…

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SPIA
Desktop

SPIA Signaling Pathway Impact Analysis

Combines the evidence obtained from the classical enrichment analysis with a…

Combines the evidence obtained from the classical enrichment analysis with a novel type of evidence, which measures the actual perturbation on a given pathway under a given condition. A bootstrap…

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CePa
Desktop
Web

CePa

An R package aiming to find significant pathways through network topology…

An R package aiming to find significant pathways through network topology information. The package has several advantages compared with current pathway enrichment tools. First, pathway node instead…

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PRS software
Desktop

PRS software Pathway Regulation Score Software

Allows to run a pathway enrichment analysis using two different approaches:…

Allows to run a pathway enrichment analysis using two different approaches: pathway regulation score (PRS) and z-score. PRS software also permits to analyze microarray gene expression data. It offers…

GOToolBox
Web

GOToolBox

Provides a series of programs allowing the functional investigation of groups…

Provides a series of programs allowing the functional investigation of groups of genes, based on the Gene Ontology resource. GOToolBox allows 1) the identification of statistically relevant over- or…

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GenePEN
Desktop

GenePEN Gene Pairwise Elastic Net

Extracts connected gene groups across the whole regularization path. GenePEN…

Extracts connected gene groups across the whole regularization path. GenePEN identifies gene selections which share significantly more connections within a molecular interaction network while…

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AMBIENT
Desktop

AMBIENT Active Modules for Bipartite Networks

Analyzes high-throughput data in the context of metabolic models. AMBIENT…

Analyzes high-throughput data in the context of metabolic models. AMBIENT allows users to find metabolic subnetworks that are significantly affected by a given genetic or environmental change. It…

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TEAK
Desktop

TEAK Topology Enrichment Analysis frameworK

An innovative approach to detect activated subpathways. First, TEAK uses an…

An innovative approach to detect activated subpathways. First, TEAK uses an in-house graph traversal algorithm to extract all root to leaf linear subpathways of a given pathway. Its major…

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ProfCom
Web

ProfCom Profiling of complex functionality

A web-based tool for the interpretation of genes that were identified to be…

A web-based tool for the interpretation of genes that were identified to be functionally linked by experiment. ProfCom automatically generates statistically valid hypotheses/biological models from…

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GO-MEP
Desktop

GO-MEP Gene Ontology-based Missing Enzyme Predictor

Aims to identify missing genes. GO-MEP takes account of gene expression,…

Aims to identify missing genes. GO-MEP takes account of gene expression, phylogenetic profile and function association scores. Besides, it uses Co-occurrence Association Score (CAS) and PubMed…

GOSim
Desktop

GOSim

Allows to calculate the functional similarity of genes based on various…

Allows to calculate the functional similarity of genes based on various information theoretic similarity concepts for GO terms. GOSim extends existing tools by providing additional lately developed…

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TopGO
Desktop

TopGO

Offers different tools for testing gene ontology (GO) terms according to the…

Offers different tools for testing gene ontology (GO) terms according to the topology of the GO graph. TopGO allows using several test statistics and methods for remove local similarities and…

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BLMA
Desktop

BLMA

Provides a bi-level meta-analysis (BLMA) framework that can be applied in a…

Provides a bi-level meta-analysis (BLMA) framework that can be applied in a wide range of applications: functional analysis, pathway analysis, differential expression analysis, and general hypothesis…

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MORPH
Desktop
Web

MORPH MOdule guided Ranking of candidate PatHway genes

An algorithm for revealing missing genes in biological pathways, and…

An algorithm for revealing missing genes in biological pathways, and demonstrate its capabilities. MORPH supports the analysis in tomato, Arabidopsis and the two new species: rice and the newly…

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DEGraph
Desktop

DEGraph

Implements recent hypothesis testing methods which directly assess whether a…

Implements recent hypothesis testing methods which directly assess whether a particular gene network is differentially expressed between two conditions. This is to be contrasted with the more…

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topologyGSA
Desktop

topologyGSA

Using Gaussian graphical models we propose a novel approach to perform pathway…

Using Gaussian graphical models we propose a novel approach to perform pathway analysis using gene expression. Given the structure of a graph (a pathway) we introduce two statistical tests to compare…

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DRWPClass
Desktop

DRWPClass

A pathway-based disease classification method. DRWPClass incorporates directed…

A pathway-based disease classification method. DRWPClass incorporates directed pathway topological information to infer reproducible pathway activities by directed random walk (DRW) and uses them for…

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TopoGSA
Web

TopoGSA Topology-based Gene Set Analysis

A web-application dedicated to the computation and visualization of network…

A web-application dedicated to the computation and visualization of network topological properties for gene and protein sets in molecular interaction networks. Different topological characteristics,…

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EnrichNet
Web

EnrichNet

Enables a direct molecular interpretation of how a user-defined set of…

Enables a direct molecular interpretation of how a user-defined set of genes/proteins is related to a gene/protein set of known function. EnrichNet is an integrative enrichment analysis method. It…

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ACST
Desktop

ACST Analysis of Consistent Signal Transduction

A method for detection of deregulated signaling pathways using microarray gene…

A method for detection of deregulated signaling pathways using microarray gene expression data. ACST incorporates information about pathway topology, as well as about the position of every gene in…

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THINK Back
Desktop

THINK Back

A set of tools that provide a robust gene set enrichment testing analysis of…

A set of tools that provide a robust gene set enrichment testing analysis of microarray data, using pathways as a source of biological knowledge. The goal of these tools is to derive high-quality…

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GrAPPA
Web

GrAPPA Graph Algorithms Pipeline for Pathway Analysis

Provides a visualization tool for graph theoretical analysis. GrAPPA is a…

Provides a visualization tool for graph theoretical analysis. GrAPPA is a web-based application that contains combinatorial methods integrated into a complete microarray analysis toolchain, from…

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PathNet
Desktop

PathNet Pathways based on Network information

A method for identifying enrichment and association between canonical pathways…

A method for identifying enrichment and association between canonical pathways in the context of gene expression data. PathNet utilizes the connectivity information in canonical pathway descriptions…

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PWEA
Desktop

PWEA Pathway Enrichment Analysis

Detects differentially expressed topological pathways among gene expression…

Detects differentially expressed topological pathways among gene expression profiles. PWEA's visualization is generated by VisANT.

MetaCore
Web

MetaCore

Accelerates discovery research with systems biology content, analytics, and…

Accelerates discovery research with systems biology content, analytics, and expertise. MetaCore is an integrated software suite for functional analysis of Next Generation Sequencing (NGS), gene…

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IPA
Desktop

IPA Ingenuity Pathway Analysis

Allows analysis, integration, and interpretation of data derived from omics…

Allows analysis, integration, and interpretation of data derived from omics experiments. IPA is a web-based software application which identifies key regulators and activity to explain expression…

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PFSNet
Web

PFSNet

Recognizes smaller parts of pathways and underlines that significant…

Recognizes smaller parts of pathways and underlines that significant subnetworks. PFSNet was tested on six datasets from three disease types. It is able to give high subnetwork-level agreement. The…

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PaLS
Web

PaLS PAthway and Literature Strainer

Allows users to work about protein identifiers or a list/set of gene and…

Allows users to work about protein identifiers or a list/set of gene and identifies which ones share certain descriptors. PaLS helps researchers in their genomic analysis, improving the potential…

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TAPPA
Desktop

TAPPA

Allows to identify phenotype-associated genetic pathways which utilize the…

Allows to identify phenotype-associated genetic pathways which utilize the pathway topological measures. The main functions of TAPPA include: (1) prioritize pathways associated with discrete or…

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POSOC
Desktop

POSOC POSet Ontology Categorizer

Provides a set of modules supporting ontology representation, mathematical…

Provides a set of modules supporting ontology representation, mathematical analysis of structures, categorization of nodes in an ontology. POSOC is a software that also furnishes evaluation of the…

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PathOlogist
Desktop

PathOlogist

Allows to transform large sets of gene expression data into quantitative…

Allows to transform large sets of gene expression data into quantitative descriptors of pathway-level behavior. PathOlogist analyzes genetic data within the context of molecular pathways. It aims to…

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GO-2D
Desktop

GO-2D Gene Ontology-2D

Finds 2-dimensional (2D) functional modules for studying complex human…

Finds 2-dimensional (2D) functional modules for studying complex human diseases. GO-2D adopts the standard methods of Bonferroni correction and false discovery rate (FDR) control, which are usually…

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