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Signaling pathway analysis (omic data)

Signaling pathways are chemical reactions in a cell from a stimulus to the response.
Curator: Susan Calhoun

HRGRN
Dataset

HRGRN

Offers a way to search and discover the relationships among genes, proteins,…

Offers a way to search and discover the relationships among genes, proteins, compounds and small RNAs in plant signal transduction, metabolism and gene regulatory networks. HRGRN models the…

Transpath
Dataset

Transpath

Contains cellular events in humans, mice, and rats, collected from over 31,500…

Contains cellular events in humans, mice, and rats, collected from over 31,500 publications. Transpath offers information about the intracellular signaling pathways. It allows the user to see details…

OmniPath
Dataset

OmniPath

Contains a comprehensive collection of literature curated human signaling…

Contains a comprehensive collection of literature curated human signaling pathways. OmniPath develops a uniform representation of the data that includes references, directionality, sign and…

pathDIP
Dataset

pathDIP pathway Data Integration Portal

An annotated database of signaling cascades. PathDIP integrates data from 20…

An annotated database of signaling cascades. PathDIP integrates data from 20 source pathway databases, comprising core pathways from major curated pathways databases, and extended pathways predicted…

Aging Chart
Dataset

Aging Chart

A wiki-based visual encyclopedia of aging processes that will facilitate rapid…

A wiki-based visual encyclopedia of aging processes that will facilitate rapid exploration of aging pathways and mechanisms by experts and entrants to the field alike. Building on an initial content…

MetaboSignal
Desktop

MetaboSignal

Allows merging metabolic and signaling pathways reported in the Kyoto…

Allows merging metabolic and signaling pathways reported in the Kyoto Encyclopaedia of Genes and Genomes (KEGG). MetaboSignal is a network-based approach designed to navigate through topological…

iPanda
Desktop

iPanda in silico Pathway Activation Network Decomposition Analysis

Identifies biomarker using gene expression data. The iPANDA method combines…

Identifies biomarker using gene expression data. The iPANDA method combines precalculated gene coexpression data with gene importance factors based on the degree of differential gene expression and…

rxncon
Desktop

rxncon

Allows to build, visualize and model cellular signal transduction networks. The…

Allows to build, visualize and model cellular signal transduction networks. The rxncon language enables the description of these networks. The rxncon software tool interprets the rxncon language and…

ACSN
Dataset

ACSN Atlas of Cancer Signalling Network

Describes in detail signalling and regulatory molecular processes that occur in…

Describes in detail signalling and regulatory molecular processes that occur in a healthy mammalian cell. ACSN is characterized by several features: (i) it is a comprehensive description of cancer…

PathoPlant
Dataset

PathoPlant

A database on plant-pathogen interactions and components of signal transduction…

A database on plant-pathogen interactions and components of signal transduction pathways related to plant pathogenesis.

NetDecoder
Desktop
Web

NetDecoder

A network biology-based computational platform designed to integrate…

A network biology-based computational platform designed to integrate transcriptomes, interactomes and gene ontologies to identify phenotype-specific subnetworks. NetDecoder is based on network flow…

SIGNOR
Dataset

SIGNOR SIGnaling Network Open Resource

Organizes and stores in a structured format signaling information published in…

Organizes and stores in a structured format signaling information published in the scientific literature. The captured information is stored as binary causative relationships between biological…

MaBoSS
Desktop

MaBoSS

Provides a simulation software for continuous time Boolean modeling. MaBoSS has…

Provides a simulation software for continuous time Boolean modeling. MaBoSS has been developed to answer specific needs of modelers. It can be combined with its associated environment and used into…

PathBuilder
Desktop

PathBuilder

Enables annotation of molecular events including protein–protein interactions…

Enables annotation of molecular events including protein–protein interactions (PPIs), enzyme–substrate relationships and protein translocation events either manually or through automated…

FASPAD
Desktop

FASPAD Fast Signaling Pathway Detection

Allows users to identify candidates for signaling pathways in protein…

Allows users to identify candidates for signaling pathways in protein interaction networks. FASPAD provides a graphical display of candidates and permits to produce an overlay of several candidates…

CBN
Dataset

CBN Causal Biological Networks database

Gathers information about biological expression language (BEL)-scripted causal…

Gathers information about biological expression language (BEL)-scripted causal network models that describe signaling pathways relevant in diseased and non-diseased pulmonary and vascular tissues.…

SignaFish
Dataset

SignaFish

An integrated resource to analyze signaling pathway cross-talks, miRNAs and…

An integrated resource to analyze signaling pathway cross-talks, miRNAs and regulatory enzymes in zebrafish. SignaFish contains more than 200 curation-based signaling interactions, 132 further…

CL
Web

CL Cancer Landscapes

Provides data-derived statistical network models for 8 human cancers. CL…

Provides data-derived statistical network models for 8 human cancers. CL contains several functions for biological interpretability of the network models, such as pathway analysis, drug-target…

SiGNet
Desktop

SiGNet Signal Generator for Networks

Enables researchers to create realistic, bespoke benchmarking datasets for the…

Enables researchers to create realistic, bespoke benchmarking datasets for the evaluation of signaling network inference. SiGNet users can specify the type and strength of interactions within a…

G T A T C G C T A
Worm Single…
Desktop

Worm Single Cell

Infers signalling networks at cellular level for cell fate specification based…

Infers signalling networks at cellular level for cell fate specification based on multiple data types, including single-cell gene expression data, PPI data, PDI data and Genetic Interaction (GI)…

Moksiskaan
Desktop

Moksiskaan

A computational platform that can be used to integrate information about the…

A computational platform that can be used to integrate information about the connections between genes, proteins, pathways, drugs, and other biological entities. The database is used to combine…

PathJam
Web

PathJam

A public tool which provides an intuitive and user-friendly framework for…

A public tool which provides an intuitive and user-friendly framework for biological pathway analysis of human gene lists. This server integrates pathway-related annotations from several public…

sigNetTrainer
Desktop

sigNetTrainer

Permits to interrogate and train signaling networks based on measurements from…

Permits to interrogate and train signaling networks based on measurements from stimulus-response experiments. sigNetTrainer is based on Integer Linear Programming (ILP) to predict the possible…

TSLP signaling pathway map
Dataset

TSLP signaling pathway map Thymic stromal lymphopoietin signaling pathway map

Provides signal transduction pathways in humans. TSLP signaling pathway map is…

Provides signal transduction pathways in humans. TSLP signaling pathway map is a manually curated resource made with PathVisio, a pathway drawing software. This map resource provides a map that…

SpliceNet
Desktop

SpliceNet

A method to infer isoform-specific co-expression networks from exon-level…

A method to infer isoform-specific co-expression networks from exon-level RNA-Seq data, using large dimensional trace. SpliceNet goes beyond differentially expressed genes and infers splicing isoform…

ScaPD
Dataset

ScaPD Scaffold Protein Database

Provides an information’s repository for scaffold proteins and associated…

Provides an information’s repository for scaffold proteins and associated signaling pathways. ScaPD contains more than 270 scaffold proteins and over 1100 distinct scaffold-mediated phosphorylation…

DISNOR
Dataset

DISNOR

Supports the assembly of disease-related signaling networks to help infer the…

Supports the assembly of disease-related signaling networks to help infer the pathways disrupted in any specific disease. DISNOR is a resource that links disease-associated genes (extracted from the…

TENET
Desktop

TENET

A network-based approach that characterizes known targets in signaling networks…

A network-based approach that characterizes known targets in signaling networks using topological features. TENET first computes a set of topological features and then leverages a SVM-based approach…

PATHiWAYS
Web

PATHiWAYS

A web tool for the interpretation of the consequences of the combined changes…

A web tool for the interpretation of the consequences of the combined changes in expression levels of genes in the context of signaling pathways. Specifically, this tool allows the user to identify…

iPathwayGuide
Web

iPathwayGuide

Allows users to quickly visualize their data through these analyses: gene…

Allows users to quickly visualize their data through these analyses: gene analysis, gene ontology, pathway analysis, drug interactions, over-represented diseases and much more. Unlike other pathway…

NetPath
Dataset

NetPath

A resource of signal transduction pathways in humans. NetPath provides detailed…

A resource of signal transduction pathways in humans. NetPath provides detailed maps of a number of immune signalling pathways, which include approximately 1600 reactions annotated from the…

ISP
Desktop

ISP Insulin signalling pathway

A comprehensive model of the insulin signalling pathway, which integrates three…

A comprehensive model of the insulin signalling pathway, which integrates three models previously available in the literature by using the rule-based modelling (RBM) approach. RBM allows for a simple…

BowTieBuilder
Web

BowTieBuilder

Infers signal transduction pathways given multiple source and/or target…

Infers signal transduction pathways given multiple source and/or target proteins. BowTieBuilder is used to infer a signaling pathway of the innate immune response in humans and a signaling pathway…

REPAIRtoire
Dataset

REPAIRtoire

A comprehensive database resource for systems biology of DNA damage and repair.…

A comprehensive database resource for systems biology of DNA damage and repair. REPAIRtoire collects and organizes the following types of information: (i) DNA damage linked to environmental mutagenic…

DDRprot
Dataset

DDRprot DNA Damage Response proteins

Integrates manually curated information on the human DNA damage response…

Integrates manually curated information on the human DNA damage response network and its sub-pathways. DDRprot is presented within an evolutionary framework that allows many features to be explored…

NsRRR
Desktop

NsRRR Network-guided sparse Reduced-Rank Regression

A multivariate regression model capable of using prior biological knowledge…

A multivariate regression model capable of using prior biological knowledge expressed as gene interaction networks to guide the search for associations between gene expression and DNA methylation…

Sorad
Desktop

Sorad

Estimates the structure of signal transduction networks and the associated…

Estimates the structure of signal transduction networks and the associated continuous signaling dynamics from phosphoprotein time-course measurements. Sorad can identify experimental conditions that…

NetAtlas
Desktop

NetAtlas

Examines signaling networks in the context of tissue gene expression patterns.…

Examines signaling networks in the context of tissue gene expression patterns. The tissue gene expression data available through NetAtlas consists of 79 human tissues, 61 mouse tissues, and 44…

PathCards
Dataset

PathCards

Stores human biological pathways and their annotations. PathCards is an online…

Stores human biological pathways and their annotations. PathCards is an online compendium based on the GeneCards database, presenting SuperPath-related data in each page, enabling quick in-depth…

CellFateScout
Desktop

CellFateScout

Uses the method of Latent Variables to turn differential high-throughput…

Uses the method of Latent Variables to turn differential high-throughput expression data and a functional network into a list of active signaling pathways. CellFateScout is a network-based…

PathwayLinker
Web

PathwayLinker

Provides a first estimate of the possible signaling effects of such changes,…

Provides a first estimate of the possible signaling effects of such changes, e.g., drug or microRNA treatments. PathwayLinker minimizes the users' efforts by integrating protein-protein…

SignaLink
Web

SignaLink

A signaling pathway resource with multi-layered regulatory networks. Users can…

A signaling pathway resource with multi-layered regulatory networks. Users can effectively analyze signaling pathways, scaffold proteins, modifier enzymes, transcription factors and miRNAs that are…

B-RGPs
Desktop

B-RGPs Branch-Recombinant Gaussian Processes

Allows inference of arbitrarily complex branching and recombination processes.…

Allows inference of arbitrarily complex branching and recombination processes. B-RGPs is a comprehensive framework that infers branching and recombination processes which are arbitrarily complex both…

SigTran
Desktop

SigTran

Helps to realize analysis and simulations of complex signal transduction…

Helps to realize analysis and simulations of complex signal transduction networks.

Solvary
Desktop

Solvary

An application for the development and analysis of complex mathematical models…

An application for the development and analysis of complex mathematical models with emphasis on models of gene signaling pathways. Solvary includes a method that allows defining some of the model…

INOH
Dataset

INOH Integrating Network Objects with Hierarchies

A highly structured, manually curated database of signal transduction pathways…

A highly structured, manually curated database of signal transduction pathways including Mammalia, Xenopus laevis, Drosophila melanogaster, Caenorhabditis elegans and canonical. Since most pathway…

MirOB
Dataset

MirOB MicroRNA OncoBase

MicroRNA targets database and data analysis and visualization tool. An…

MicroRNA targets database and data analysis and visualization tool. An integrative instrument for dissecting complex role microRNA in cancer. The Database includes more than 8500 manually curated…

AraPath
Dataset

AraPath

A knowledgebase for pathway analysis in Arabidopsis. To create a knowledgebase…

A knowledgebase for pathway analysis in Arabidopsis. To create a knowledgebase for plant pathway analysis, 1683 lists of differentially expressed genes were collected from 397 gene-expression…

CellPublisher
Web
Desktop

CellPublisher

A web app to improve the navigation of biological pathways. CellPublisher…

A web app to improve the navigation of biological pathways. CellPublisher converts diagrams into fully-featured maps that live inside a browser. The main purpose of this tool is to provide an easier…

A A A
The aMAZE…
Dataset

The aMAZE LightBench

A web interface to the aMAZE relational database, which contains information on…

A web interface to the aMAZE relational database, which contains information on gene expression, catalysed chemical reactions, regulatory interactions, protein assembly, as well as metabolic and…

HSPD
Dataset

HSPD Hedgehog Signaling Pathway Database

A curated repository of information pertaining to the Hedgehog developmental…

A curated repository of information pertaining to the Hedgehog developmental pathway. The Hedgehog Signaling Pathway Database is designed to provide centralized access to a wide range of relevant…

PathPPI
Dataset

PathPPI

An integrated dataset of human pathways and protein-protein interactions. We…

An integrated dataset of human pathways and protein-protein interactions. We developed a series of rules for transforming protein interactions from pathway to binary model, and the protein…

CSNDB
Dataset

CSNDB Cell-signaling networks database

Includes all the biological properties of cellular signal transduction,…

Includes all the biological properties of cellular signal transduction, including biological reactions that transfer cellular signals and molecular attributes characterized by sequences, structures,…

PathwayGuide
Desktop

PathwayGuide

It is the most advanced standalone pathway analysis application available.…

It is the most advanced standalone pathway analysis application available. Similar to iPathwayGuide, it also considers the size, role, and position of each gene on the pathway as it models…

PathArt
Dataset

PathArt

A database of manually curated biomolecular interactions with specific focus on…

A database of manually curated biomolecular interactions with specific focus on signaling and metabolic pathways in disease conditions.

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