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

HRGRN HRGRN

HRGRN

A graph-based database to search and discover the relationships among genes,…

A graph-based database to search and discover the relationships among genes, proteins, compounds and small RNAs in plant signal transduction, metabolism and gene regulatory networks. HRGRN not only…

Desktop app
MetaboSignal MetaboSignal

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…

pathway Data… pathway Data Integration Portal

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 Aging Chart

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…

Desktop app
CellNetOptimizer CellNetOptimizer

CellNOpt CellNetOptimizer

An open-source R software package for building predictive logic models of…

An open-source R software package for building predictive logic models of signaling networks by training networks derived from prior knowledge to signaling (typically phosphoproteomic) data.…

Desktop app
CellFateScout CellFateScout

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…

Desktop app
NetAtlas NetAtlas

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…

Desktop app
G T A T C G C T A Worm Single Cell Worm Single Cell

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)…

Desktop app
in silico Pathway… in silico Pathway Activation Network…

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…

NetPath NetPath

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…

Desktop app
Solvary Solvary

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…

REPAIRtoire REPAIRtoire

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…

DNA Damage Response… DNA Damage Response proteins

DDRprot DNA Damage Response proteins

A database that integrates manually curated information on the human DNA damage…

A database that 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…

PathPPI PathPPI

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…

Desktop app
Insulin signalling… Insulin signalling pathway

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…

Desktop app
Web app
NetDecoder NetDecoder

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…

SignaFish SignaFish

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…

SIGnaling Network… SIGnaling Network Open Resource

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…

Desktop app
TENET TENET

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…

Web app
Cancer Landscapes Cancer Landscapes

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…

Web app
PathwayLinker PathwayLinker

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…

Web app
PATHiWAYS PATHiWAYS

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…

Web app
PathJam PathJam

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…

PathCards PathCards

PathCards

An integrated database of human biological pathways and their annotations.…

An integrated database of human biological pathways and their annotations. Human pathways were clustered into SuperPaths based on gene content similarity. Each PathCard provides information on one…

Desktop app
SpliceNet SpliceNet

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…

Web app
SignaLink SignaLink

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…

Web app
iPathwayGuide iPathwayGuide

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…

Desktop app
Network-guided sparse… Network-guided sparse Reduced-Rank Regression

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…

MicroRNA OncoBase MicroRNA OncoBase

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…

Desktop app
Moksiskaan Moksiskaan

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…

Web app
Desktop app
CellPublisher Deprecated CellPublisher

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…

Integrating Network… Deprecated Integrating Network Objects with Hierarchies

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…

Hedgehog Signaling… Deprecated Hedgehog Signaling Pathway Database

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…

Cell-signaling… Deprecated Cell-signaling networks database

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,…

Desktop app
PathwayGuide Deprecated PathwayGuide

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 Deprecated PathArt

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.

AraPath Deprecated AraPath

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…

Curators for Signaling pathways

  • Susan Calhoun's avatar image
    Susan Calhoun
    New York University, New York, NY,…
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