We actively seek collaborations with other data resources and users to improve data integration, share efforts, and make our data maximally useful to biologists and bioinformaticians. Here are a list of software tools, websites, databases and research projects that: i) support the use of Reactome data, ii) have integrated Reactome data, or iii) provide data linkages to the Reactome website.
If we are missing your website, database, software tool and project, please contact our This email address is being protected from spambots. You need JavaScript enabled to view it..
Name |
Description |
---|---|
ABACUS |
ABACUS is an Algorithm based on a BivAriate CUmulative Statistic to identify single nucleotide polymorphisms (SNPs) significantly associated with a disease within predefined sets of SNPs such as pathways or genomic regions |
AbsIDconvert |
AbsIDconvert is an absolute approach for converting genetic identifiers at different granularities |
ADaCGH |
ADaCGH is a parallelized web-based application and R package for the analysis of aCGH data |
AgBase |
AgBase is a functional genomics resource for agriculture |
Algal Functional Annotation Tool |
Algal Functional Annotation Tool is a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data |
AltAnalyze |
AltAnalyze is a platform for analyzing and visualizing exon expression data |
AMMO_Prot |
AMMO-Prot is an amine system project 3D-model finder |
Annotate-it |
Annotate-it is a Swiss-knife approach to annotation, analys is and interpretation of single nucleotide variation in human disease |
Arabidopsis Reactome |
Arabidopsis Reactome is a curated knowledgebase of plant biological pathways that contains many plant pathways curated by the John Innes Centre team, plus plant pathways imported from AraCyc and KEGG |
ARACNe |
ARACne is an Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context |
Asterias |
Asterias includes applications for the analysis of genomic and proteomic data that cover from data normalization to development of prediction models for survival data |
atBioNet |
atBioNet is an integrated network analysis tool for genomics and biomarker discovery |
Atlas of Genetics and Cytogenetics in Oncology and Haematology |
The Atlas of Genetics and Cytogenetics in Oncology and Haematology is a peer reviewed on-line journal and database in free access on internet devoted to genes, cytogenetics, and clinical entities in cancer, and cancer-prone diseases |
AutismKB |
An evidence-based knowledgebase of autism genetics |
Babelomics |
Babelomics is a complete suite of web tools for the analysis, integration and interpretation of different types of genomic data |
Baysian Pathway Analysis |
A computational method to identify significant pathways from microarray data with samples from test and control classes |
BcCluster |
BcCluster is a Bladder Cancer Database at the Molecular Level |
BCML |
The biological Connection Markup Language is a SBGN-compliant format for visualization, filtering and analysis of biological pathways |
BIANA |
Biological interactions and network analysis (BIANCA) is a software framework for compiling biological interactions and analyzing networks |
BindingDB |
A public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules |
BiNoM |
Biological Network Manager is a Cytoscape plug-in, developed to facilitate the manipulation of biological networks represented in standard systems biology formats (SBML, SBGN, BioPAX) |
Bio3graph |
Automated extraction of biological relations from the literature, resulting in a set of (component1, reaction, component2) triplets and composing a graph structure which can be visualised, compared to the manually constructed topology and examined by the experts |
BioBin |
BioBin is a bioinformatics tool for automating the binning of rare variants using publicly available biological knowledge |
BioDB |
BioDB is an ontology-enhanced information system for heterogeneous biological information |
BioDWH |
BioDWH is a Data Warehouse Kit for Life Science Data Integration |
Biofilter |
Biofilter is a knowledge-integration system for the multi-locus analysis of genome-wide association studies |
biofilter 2.0 |
A single interface for accessing multiple publicly available human genetic data sources that have been compiled in the supporting database of Library of Knowledge Integration (LOKI) |
BioGPS |
BioGPS is a free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function |
BioGRID |
The Biological General Repository for Interaction Datasets (BioGRID) database was developed to house and distribute collections of protein and genetic interactions from major model organism species |
BioHealthBase BRC |
BioHealthBase Bioinformatics Resource Center (BRC) is a public bioinformatics database and analysis resource for the study of specific biodefense and public health pathogens-Influenza virus, Francisella tularensis, Mycobacterium tuberculosis, Microsporidia species and ricin toxin |
BioJS |
BioJS is an open source standard for biological visualisation |
BiologicalNetworks |
Data integration and network based research environment with tools for inference and analysis of gene regulatory modules |
BioMart |
BioMart enables scientists to perform advanced querying of biological data sources through a single web interface |
BioMoby |
BioMOBY is an Open Source research project which aims to generate an architecture for the discovery and distribution of biological data through web services |
BioModels |
BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests |
BioMyn |
BioMyn is an integrated human gene and protein knowledgebase |
BioPAX |
Biological Pathway Exchange (BioPAX) is a RDF/OWL-based standard for the exchange of biological pathways |
BioPAX Cytoscape PlugIn |
BioPAX Cytoscape PlugIn enables Cytoscape users to load and visually render BioPAX files from the web or a local file system; distributed with Reactome sample files |
BioPP |
BioPP is a tool for web-publication of biological networks |
BioProfiling.de |
BioProfiling de provides a common interface for a collection of recently developed analytical tools for genomics, proteomics and metabolimics data |
BioSemantic |
BioSemantic is a framework that was designed to speed integration of relational biological databases |
Biovista |
Systematic drug repositioning capability offers decision makers a reliable tool for pipeline optimization, asset protection and life cycle management |
BioWisdom SRS |
BioWisdom Sequence Retrival System (SRS) is a proven and scalable data integration platform delivering genomic data to thousands of users |
BirdsEyeView |
Visualizing experimental transcriptomic data using different views that users can switch among and compare |
BirdsEyeView |
BirdsEyeView (BEV) is a graphical overviews of experimental data |
BisoGenet |
BisoGenet is a Cytsocape app for gene network building, visualization and analysis |
BNP |
Bayesian Network Prior (BNP) depicts the relation between various evidence types that contribute to the event gene interaction and is used to calculate the probability of a candidate graph (G) in the structure learning process |
BowTieBuilder |
BowTieBuilder is aModeling signal transduction pathways |
C2Cards - Human |
Consensus and Conflict Cards (C2Cards) provides concise overviews of what pathway databases do or do not agree on |
caBIG |
cancer Biomedical Informatics Grid¬ caBIG¬ is an information network enabling all constituencies in the cancer community _ researchers, physicians, and patients _ to share data and knowledge |
CAERUS |
CAERUS predicts CAncER oUtcomeS Using Relationship between Protein Structural Information, Protein Networks, Gene Expression Data, and Mutation Data |
CancerResource |
CancerResource is a comprehensive database of cancer-relevant proteins and compound interactions supported by experimental knowledge |
CANGES |
CANGES provides a means to rapidly identify networks for any set of genes and generate novel hypotheses |
canSAR |
canSAR is an integrated cancer public translational research and drug discovery resource |
CardioNet |
A human metabolic network suited for the study of cardiomyocyte metabolism |
CardioNet |
CardioNet is a human metabolic network suited for the study of cardiomyocyte metabolism |
CardioVINEdb |
CardioVINEdb is a data warehouse approach for integration of life science data in cardiovascular diseases |
CCDB |
Cell Cycle Database is a collection of genes and proteins involved in human and yeast cell cycle |
CEGP |
Cancer Gene Encyclopedia will allow scientists to identify new cancer targets |
Cell Cycle Ontology |
The Cell Cycle Ontology is an application ontology for the representation and integrated analysis of the cell cycle process |
Cell Illustrator |
Cell Illustrator is an environment for simulating and representing biological systems |
CellBase |
CellBase is a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources |
CellCircuits |
CellCircuits is a database of protein network models |
CellDesigner |
CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks |
CellFrame |
CellFrame is a data structure for abstraction of cell biology experiments and construction of perturbation networks |
Characterization Tool |
The Characterization Tool is a novel knowledge-based database and web application that allows the storage and analysis of various kinds of data associated with cell, cell line and tissue characterization across different species |
ChEBI |
Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds |
Chem2Bio2RDF |
Chem2Bio2RDF is a semantic framework for linking and data mining chemogenomic and systems chemical biology data |
ChemProt |
ChemPort is a disease chemical biology database, which is based on a compilation of multiple chemical_protein annotation resources, as well as disease-associated protein_ protein interactions |
ChiBE |
Chisio BioPAX Editor (ChiBE) is a free editing and visualization tool for pathway models represented by the BioPAX format |
Chipster |
Chipster is a user-friendly analysis software for microarray and other high-throughput data |
CIDeR |
CIDeR is aMultifactorial interaction networks in human diseases |
CIDMS |
Cardiac Integrated Database Management System (CIDMS) integrates the heterogeneous -omic data (available from multitude of sources and in various formats such as publication and associated supplementary files, databases and web pages) that are generated at different biological levels |
Cluepedia |
CluePedia provides insights into pathways by integrating experimental and in silico information |
CMS |
A Web-Based System for Visualization and Analysis of Genome-Wide Methylation Data of Human Cancers |
COFECO |
COFECO is a web-based tool for a composite annotation of protein complexes |
ConsensusPathDB |
ConsensusPathDB is a database system for the integration of human functional interactions |
COPASI |
COPASI is a software application for simulation and analysis of biochemical networks and their dynamics |
cPath |
cPath is an open source pathway database and software suite designed for systems biology research |
CPNM |
Context-specific Protein Network Miner derives context-specific PPI networks in real-time from the PubMed database based on a set of user-input keywords and enhanced PubMed query system |
CSAX |
Characterizing Systematic Anomalies in eXpression Data (CSAX) aids in both identifying anomalies and explaining the underlying biology in expression datasets |
CTD |
The Comparative Toxicogenomics Database (CTD) is a curated database that promotes understanding about the effects of environmental chemicals on human health |
CTSA Pharmaceutical Assests Portal |
The Pharmaceutical Assets Portal aims to facilitate industry-academic collaborations for discovery of new indications for compounds no longer being developed by pharmaceutical companies, through eliminating barriers to access such compounds |
CyTargetLinker |
A Cytoscape App to Integrate Regulatory Interactions in Network Analysis |
Cytoscape |
Cytoscape is a free software package for visualizing, modeling and analyzing molecular and genetic interaction networks |
DAPD |
DAPD is a knowledgebase for Diabetes Associated Proteins |
DAPPER |
DAPPER is a data-mining resource for protein-protein interactions |
DAPPLE |
Disease Association Protein-Protein Link Evaluator (DAPPLE) looks for significant physical connectivity among proteins encoded for by genes in loci associated to disease according to protein-protein interactions reported in the literature |
DAVID |
Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes |
DawnRank |
DawnRank is a discover tool for personalized driver genes in cancer |
dbOGAP |
dbOGAP is a Database of O-GlcNAcylated Proteins and Sites |
DC-ATLAS |
DC-ATLAS is a systems biology resource to dissect receptor specific signal transduction in dendritic cells |
DDEC |
Dragon Database of genes implicated in Esophageal Cancer (DDEC) is an integrated knowledge database aimed at representing a gateway to esophageal cancer related data |
DDESC |
DDESC is Dragon database for exploration of sodium channels in humans, |
DDPC |
Dragon Database of Genes associated with Prostate Cancer (DDPC) is an integrated knowledge database aimed at representing a gateway to prostate cancer related data |
DECODE |
DECODE is an integrated differential co-expression and differential expression analysis of gene expression data |
DeDaL |
DeDaL is a Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts |
DEEP |
DEEP is a tool for differential expression effector prediction |
DESHCV |
Dragon Exploratory System on Hepatitis C Virus (DESHCV) is a biomedical text-mining and relationship exploring knowledgebase is the first reported comprehensive Hepatitis C Virus (HCV) |
DESSCD |
Dragon Exploration System for Sickle Cell Disease permits the exploration of text-mined and data-mined information about SCD |
DESTAF |
Dragon Exploration System for Toxicants and Fertility (DESTAF) is a specialized, public resource specifically aimed at researchers investigating reproductive toxicity |
DICS |
The DICS database is a dynamic web repository of computationally predicted functional modules from the human protein-protein interaction network |
Dintor |
Dintor is a data integration framework that provides a set of over 30 tools to assist researchers in the exploration of genomics and proteomics datasets |
Discovery-2 |
An interactive resource for the rational selection and comparison of putative drug target proteins in malaria Phelelani T |
DisGeneNet |
DisGeNET is a discovery platform integrating information on gene-disease associations (GDAs) from several public data sources and the literature |
DNAtraffic |
DNAtraffic database is dedicated to be an unique comprehensive and richly annotated database of genome dynamics during the cell life |
DR-GAS |
DR-GAS is a database of functional genetic variants and their phosphorylation states in human DNA repair systems |
DriverDB: |
DriverDB is an exome sequencing database for cancer driver gene identification |
DriverNet |
DriverNet is auncovering the impact of somatic driver mutations on transcriptional networks in cancer |
DroID |
Drosophila Interactions Database is a comprehensive resource for annotated gene and protein interactions |
DrugViz |
DrugViz is a Cytoscape plugin that is designed to visualize and analyze small molecules within the framework of the interactome |
DRYGIN |
Data Repository of Yeast Genetic Interactions (DRYGIN) is a web database system that provides a central platform for yeast genetic network analysis and visualization |
ECMDB |
ECMDB is The E coli Metabolome Database |
EDdb |
Eddb is a web resource for eating disorder and its application to identify an extended adipocytokine signaling pathway related to eating disorder |
EndoNet |
EndoNet is an information resource about the intercellular signaling network |
ENFIN |
ENFIN is a network to enhance integrative systems biology |
Enrichment map |
Enrichment map is a network-based method for gene-set enrichment visualization and interpretation |
Enrichr |
Enrichr is an Interactive and collaborative HTML5 gene list enrichment analysis tool |
Enzyme Portal |
Mines and displays data about proteins with enzymatic activity from public repositories via a single search, and includes biochemical reactions, biological pathways, small molecule chemistry, disease information, 3D protein structures and relevant scientific literature |
Eu.Gene Analyzer |
Eu Gene Analyzer is a tool for integrating gene expression data with pathway databases |
Expander |
EXPression ANalyzer and DisplayER) is an integrated software platform for the analysis of gene expression data, which is freely available for academic use |
ExPASy Proteomics Server |
Expert Protein Analysis System (ExPASy) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE |
FACT |
FACT is a framework for the functional interpretation of high-throughput experiments |
FLIGHT |
FLIGHT an online resource compiling data from over 100 Drosophila in vivo and in vitro RNAi screens |
FluMap |
Comprehensive pathway map that can serve as a graphically presented knowledgebase and as a platform to analyze functional interactions between IAV and host factors |
FluxMap |
A VANTED add-on for the visual exploration of flux distributions in biological networks |
FlyMine |
FlyMine is an integrated database for Drosophila and Anopheles genomics |
FlyReactome |
FlyReactome is a curated knowledgebase of Drosophila melanogaster pathways |
fuga |
Functional Genomics Assistant is an extensible and portable MATLAB toolbox for the inference of biological relationships, graph topology analysis, random network simulation, network clustering, and functional enrichment statistics |
FunGenES |
The FunGenES database is a genomics resource for mouse embryonic stem cell differentiation |
g:Profiler |
g:Profiler is a web-based toolset for functional profiling of gene lists from large-scale experiments |
G2SBC |
Genes-to-Systems Breast Cancer (G2SBC) Database is a bioinformatics resource that collects and integrates data about genes, transcripts and proteins which have been reported in literature to be altered in breast cancer cells |
Gaggle |
Gaggle is a framework for exchanging data between independently developed software tools and databases to enable interactive exploration of systems biology data |
Gallus Genome GBrowse |
Gallus Genome GBrowse provides online access to genomic and other information about the chicken |
GallusReactome |
GallusReactome is a curated knowledgebase of chicken pathways |
GANPA |
A novel gene-weighed pathway analysis approach, as implemented in an R package called ñGene Associaqtion Network-based Pathway Analysis" |
GAP |
Gene functional Association Predictor is an integrative method for predicting and characterizing gene functional associations |
GATE |
Grid Analysis of Time-series Expression (GATE) is an integrated computational software platform for the analys is and visualization of high-dimensional bio-molecular time-series |
GBMBase |
GBMBase focuses on data used in Glioblastoma multiforme (GBM) research |
GCMAP |
GCMAP is a user-friendly connectivity mapping with R |
GEDI |
Genetic Diseases Gene Discovery (GEDI) provides integrated bioinformatics platforms that will support systems analysis of Human multigene disorders |
Gene Ontology |
The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases |
Gene3D |
Gene3D is a domain-based resource for comparative genomics, functional annotation and protein network analysis |
GeneAnswers |
Using the Bioconductor GeneAnswers Package to Interpret Gene Lists |
GeneBrowser 2 |
GeneBrowser 2 is an application to explore and identify common biological traits in a set of genes |
GeneCards |
Extracts and integrates gene-related data, including genomic, transcriptomic, proteomic, genetic, clinical, and functional information |
GeneMANIA |
Helps you predict the function of your favourite genes and gene sets |
GeneSigDB |
GeneSigDB is a manually curated database and resource for analysis of gene expression signatures |
GeneSpring |
GeneSpring GX provides powerful, accessible statistical tools for fast visualization and analysis of expression and genomic structural variation data |
GeneSrF |
GeneSrF is a web-based tool for gene selection and classification using random forest |
GeneTrail 2 |
GeneTrail 2 is a web-interface providing access to different tools for the statistical analysis of molecular signatures |
GenMAPP |
Gene Map Annotator and Pathway Profiler (GenMAPP) is a free, open-source bioinformatics software tool designed to visualize and analyze genomic data in the context of pathways (metabolic, signaling), connecting gene-level datasets to biological processes and disease |
GenomeSpace |
A cloud-based interoperability framework to support integrative genomics analysis through an easy-to-use Web interface |
GenWay Biotech, Inc. |
GenWay Biotech, Inc is a protein, antibody and ELISA solutions provider |
gespeR |
gespeR is a statistical model for deconvoluting off-target-confounded RNA interference screens |
GEYSIR |
Genomic Explorer Y Survey of Immune Response (GEYSIR) is a web application designed to correlate case-control association data with genetic and physical maps of the human genome, including key human genes associated with host immune response |
GingerSNP |
GingerSNP tools help you explore standard human SNP arrays by interaction, pathway, and function |
GLAMM |
GLAMM is a Genome-Linked Application for Metabolic Maps |
GOAL |
GOAL is a software tool for assessing biological significance of genes groups |
GOMiner |
GoMiner» is a tool for biological interpretation of 'omic' data _ including data from gene expression microarrays |
GPEC |
GPEC is a Cytoscape plug-in for random walk-based gene prioritization and biomedical evidence collection |
graphite |
A Bioconductor package to convert pathway topology to gene network |
GraphWeb |
GraphWeb is a public web server for graph-based analysis of biological networks |
GSEA |
Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states |
GuavaH |
GuavaH is a compendium of host genomic data in HIV biology and disease |
HAPMAP |
The International HapMap Project is a partnership of scientists and funding agencies from Canada, China, Japan, Nigeria, the United Kingdom and the United States to develop a public resource that will help researchers find genes associated with human disease and response to pharmaceuticals |
HCVpro |
HCVpro is a Hepatitis C virus protein interaction database |
HDAPD |
HDAPD is a web tool for searching the disease-associated protein structures |
HEFalMp |
HEFalMp (Human Experimental/FunctionAL MaPper) is a tool that allows interactive exploration of functional maps (or functional relationship networks) predicted from integration of many genome-scale experimental results |
HepatoNet1 |
HepatoNet1 is a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology |
HGNC |
The HGNC database in 2008 is a resource for the human genome |
hiPathDB |
hiPathDB is a human-integrated pathway database with facile visualization |
hLGDB |
hLGDB is a database of human lysosomal genes and their regulation |
HMDB |
The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body |
HMPAS |
Human Membrane Protein Analysis System provides comprehensive information about human membrane proteins including specific features of certain membrane protein groups |
HMPAS |
HMPAS is a Human Membrane Protein Analysis System |
HMTD |
Human Membrane Transporter Database |
HOCCLUS2 |
bicluster miRNAs and target messenger RNAs (mRNAs) on the basis of their experimentally-verified and/or predicted interactions |
HomoMINT |
HomoMINT is an inferred human network based on orthology mapping of protein interactions discovered in model organisms |
HPD |
Human Pathway Database (HPD) is an integrated human pathway database providing comprehensive and combined view connecting human proteins, genes, RNAs, enzymes, signaling, metabolic reactions and gene regulatory events |
HPIDB |
HPIDB is a unified resource for host-pathogen interactions |
Hubba |
Hubba is ahub objects analyzer--a framework of interactome hubs identification for network biology |
HuPho |
HuPho is a human phosphatase portal |
IBDsite |
A disease-oriented platform, which collects data related to biomolecular mechanisms involved in the Inflammatory Bowel Disease onset |
IDClight |
IDClight converts single IDs through an URL |
Idconverter |
Idconvertor map IDs to other known public DBs |
ImmPort |
Immunology Database and Analysis Portal (ImmPort), is a one stop shop to access reference and experiment data for immunologists |
Influenza Research Database |
Influenza Research Database is a resource for the influenza virus research community that will facilitate an understanding of the influenza virus and how it interacts with the host organism |
InnateDB |
InnateDB is a publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans and mice to microbial infection |
INOH |
Integrating Network Objects with Hierarchies (INOH) is a pathway database of model organisms including human, mouse, rat and others |
INRICH |
NRICH is an Interval-based Enrichment Analysis Tool for Genome Wide Association Studies |
IntAct |
IntAct is an open source resource for molecular interaction data |
IntegromeDB |
IntegromeDB is an integrated system and biological search engine |
Interactome3D |
A resource for the structural annotation and modeling of protein-protein interactions |
Intermine |
An open source data warehouse built specifically for the integration and analysis of complex biological data |
IPAD |
Integrated Pathway Analysis Database for Systematic Enrichment Analysis for defining inter-association between pathway, disease, drug and organ specificity |
iPAS |
iPAS is series of integrative steps, which extend existing pathway analysis techniques It consists of four parts is a data processing, gene-level statistics, individualized pathway aberrance score (iPAS) and a significance test |
IPAVS |
IPAVS is an Integrated Pathway Resources, Analysis and Visualization System |
ISAAC |
InterSpecies Analysing Application using Containers is a web based tool, which analyses sets of genes, transcripts and proteins under different biological viewpoints and to interactively modify these sets at any point of the analysis |
KaBOB |
KaBOB is an ontology-based semantic integration of biomedical databases |
KDBI |
Update of KDBI is a Kinetic data of bio-molecular interaction database |
KeyPathwayMiner |
KeyPathwayMiner is a condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape |
KOBAS 2.0 |
KOBAS is an update of KOBAS (KEGG Orthology Based Annotation System) Its purpose is to identify statistically enriched related pathways and diseases for a set of genes or proteins, using pathway and disease knowledge from multiple commonly used databases |
LDGIdb |
LDGIdb is a database of gene interactions inferred from long-range strong linkage disequilibrium between pairs of SNPs |
Linked Life Data |
Linked Life Data is a semantic integration platform for the biomedical domain |
LipidHome |
A Database of Theoretical Lipids Optimized for High Throughput Mass Spectrometry Lipidomics |
Lists2Networks |
Lists2Networks provides integrated analysis of gene/protein lists |
LiverAtlas |
LiverAtlas is a unique integrated knowledge database for systems-level research of liver and hepatic disease |
LOKI |
Library of Knowledge Integration (LOKI), which contains diverse prior knowledge from multiple collections of biological data |
MAGeCK |
MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens |
Manteia |
Manteia is a predictive data mining system for vertebrate genes and its applications to human genetic diseases |
mAPKL |
mAPKL is aR/Bioconductor package for detecting gene exemplars and revealing their characteristics |
MassVis |
MassVis is a Visual analysis of protein complexes using mass spectrometry |
MeSH |
MeSH ORA framework is aR/Bioconductor packages to support MeSH over-representation analysis |
Meta-All |
Meta-All is a system for managing metabolic pathway information |
MetaboLights |
The MetaboLights repository is a Curation challenges in metabolomics |
MetaCrop |
MetaCrop 20 is a managing and exploring information about crop plant metabolism |
METACYC |
MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways |
MetaMapp |
Mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity |
METANNOGEN |
METANNOGEN is a flexible tool to manage information for the design of metabolic networks |
MetaReg |
MetaReg is a platform for modeling, analysis and visualization of biological systems using large-scale experimental data |
metaTIGER |
metaTIGER is a collection of metabolic profiles and phylogenomic information on a taxonomically diverse range of eukaryotes |
MetNet Online |
MetNet Online is a novel integrated resource for plant systems biology |
MetNetAPI |
MetNetAPI is a flexible method to access and manipulate biological network data from MetNet |
MetRxn |
MetRxn is a knowledgebase of metabolites and reactions spanning metabolic models and databases |
MGV |
MGV is a generic graph viewer for comparative omics data |
MiMI |
Michigan Molecular Interactions (MiMI) provides access to the knowledge and data merged and integrated from numerous protein interactions databases |
MIMO |
MIMO is an efficient tool for molecular interaction maps overlap |
Mimoza |
Mimoza is a web-based semantic zooming and navigation in metabolic networks |
MINT |
MINT is a public repository for molecular interaction data |
mirDIP |
microRNA Data Integration Portal (mirDIP) integrates twelve microRNA prediction datasets from six microRNA prediction databases, allowing users to customize their microRNA target searches |
MIRIAM |
MIRIAM is an effort to standardise the Minimal Information Required In the Annotation of Models, so that different groups can collaborate on annotating and curating computational models in biology |
miRror-Suite |
miRror-Suite platform provides a concise, plausible explanation for the regulation of miRNAs in such complex settings |
miRSystem |
miRSystem is an Integrated System for Characterizing Enriched Functions and Pathways of MicroRNA Targets |
MK4MDD |
MK4MDD is a Multi-Level Knowledge Base and Analysis Platform for Major Depressive Disorder |
MMMDB |
MMMDB is a Mouse Multiple Tissue Metabolome Database |
modMine |
modMine is a flexible access to modENCODE data |
MODOMICS |
MODOMICS is a database of RNA modification pathways - 2013 update |
MoKCa |
The MoKCa (Mutations of Kinases in Cancer) database has been developed to structurally and functionally annotate, and where possible predict, the phenotypic consequences of mutations in protein kinases implicated in cancer |
MoonDB |
MoonDB is a database containing information on all the candidates identified in the analys is and a set of manually curated human moonlighting proteins |
MOPED |
Model Organism Protein Expression Database enables discoveries through consistently processed proteomics data |
MSigDB |
The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software |
MuSiC |
MuSiC is an Identifying mutational significance in cancer genomes |
MyBiosource |
MyBiosource is a provider of antibody, protein, peptide and ELISA reagents |
NaviCell |
NaviCell is a web-based environment for navigation, curation and maintenance of large molecular interaction maps |
NAViGaTOR |
A powerful graphing application for the 2D and 3D visualization of biological networks |
NCBI BioSystems |
The NCBI Biosystems database centralizes and cross-links existing biological systems databases |
NCBI Gene |
Entrez Gene is a searchable database of genes, from RefSeq genomes, and defined by sequence and/or located in the NCBI Map Viewer |
NCBO Bioportal |
BioPortal is a Web-based application for accessing and sharing biomedical ontologies |
NCIS |
NCIS is a Network-assisted Co-clustering for the Identification of cancer Subtypes |
ncRNA |
ncRNA is a portal site for bioinformatics tools and databases specialized for functional RNAs |
NeMo |
NeMo is a Network Module identification in Cytoscape |
NetBox |
NetBox is a Java-based software tool for performing network analysis on human interaction networks |
NetHiKe |
A simple knowledge-based mining method for exploring hidden key molecules in a human biomolecular network |
NetPath |
NetPath is a public resource of curated signal transduction pathways |
NetSlim |
NetSlim is a High-confidence curated signaling maps |
NetWalker |
NetWalker is a contextual network analysis tool for functional genomics |
Network |
Network Screening is a New Method to Identify Active Networks from an Ensemble of Known Networks |
Network2Canvas |
Network2Canvas is a Network Visualization on a Canvas with Enrichment Analysis |
NetWORKIN |
NetWORKIN is a method for predicting in vivo kinase-substrate relationships, that augments consensus motifs with context for kinases and phosphoproteins |
NetworkLego |
NetworkLego is a general computational framework for detecting cellular networks that are activated in a particular cell state or in response to a perturbation and for determining core cellular networks that are activated in response to multiple perturbations |
NetworkPrioritizer |
A versatile tool for network-based prioritization of candidate disease genes or other molecules |
NeuroDNet |
An open source platform for constructing and analyzing neurodegenerative disease networks |
neXtProt |
neXtProt is a human-centric discovery platform offering its users a seamless integration of and navigation through proteins-related data |
NGP |
Networked Gene Prioritizer integrates gene expression and protein-protein interaction network to prioritize cancer-associated genes |
OncoRep |
OncoRep is an n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing |
Onto-Tools |
Onto-Tools is a New additions and improvements in 2006 |
OntoSlug |
OntoSlug is a dynamic visual front-end program for ontologies |
OPHID |
Integrated known, experimental and predicted PPIs for five model organisms and human in the I2D database |
ORCID |
ORCID provides a persistent digital identifier that distinguishes you from every other researcher |
OREMPdb |
Ontology Reasoning Engine for Molecular Pathways is a semantic dictionary of computational pathway models |
p53 Knowledgebase |
The p53 Knowledgebase is an integrated information resource for p53 research |
PAGED |
PAGED is a pathway and gene-set enrichment database to enable molecular phenotype discoveries |
PAGER |
PAGER is a new database framework to perform integrative ñgene-set, network, and pathway analysisî (GNPA) |
PaLS |
PaLS is a tool that filters, from a list or a set of lists of gene/clone/protein identifiers, those that meet certain criteria related to their references to articles in PubMed, Gene Ontology terms and KEGG and Reactome pathways |
Pancreatic Expression database |
The Pancreatic Expression database is the main repository for pancreatic-derived -omics data |
Pandora |
Pandora is a novel integrated approach that uses network topology to predict biological pathways |
PARADIGM-SHIFT |
PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis |
Path2Models |
Path2Models is a Large-scale generation of computational models from biochemical pathway maps |
PathAgent |
PathAgent is a Multi-agent System for Updated Pathway Information Integration |
PathCase-SB |
PathCase-SB is integrating data sources and providing tools for systems biology research |
PathJam |
PathJam is a public tool which provides an intuitive and user-friendly framework for biological pathway analysis of human gene lists |
PATHLOGIC-S |
A Scalable Boolean Framework for Modelling Cellular Signalling |
PathNER |
Pathway Named Entity Recognition is a tool for systematic identification of biological pathway mentions in the literature |
Pathprinting |
Pathprinting is an integrative approach to understand the functional basis of disease |
PathRings |
PathRings is a web-based tool for exploration of ortholog and expression data in biological pathways |
PathScan |
PathScan is Tool for Discerning Mutational Significance in Groups of Putative Cancer Genes |
PathVar |
PathVar is analysis of gene and protein expression variance in cellular pathways using microarray data |
Pathview |
Pathview is an R/Bioconductor package for pathway-based data integration and visualization |
PathVisioRPC |
Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment |
Pathway Projector |
Pathway projector is a Web-based zoomable pathway browser using KEGG Atlas and Google Maps API |
Pathway Commons |
Pathway Commons provides researchers with convenient access to a comprehensive collection of pathways from multiple organisms |
Pathway Interaction Database |
Pathway Interaction Database (PID) is a freely available collection of curated and peer-reviewed pathways composed of human molecular signaling and regulatory events and key cellular processes |
Pathway Knowledge Base |
Pathway Knowledge Base is a public repository for searching biological pathways |
Pathway-GPS |
Pathway-GPS and SIGORA identifies relevant pathways based on the over-representation of their gene-pair signatures |
PathwayCaseMAW |
PathwayCaseMAW is an online system for metabolic network analysis |
PathwayLinker |
A system of integrating protein-protein interaction and signaling pathway data from several sources with statistical significance tests and clear visualization |
PATIKAmad |
PATIKAmad puts microarray data into pathway context |
PATIKAweb |
Pathway Analysis Tool for Integration and Knowledge Acquisition |
PaxTools |
An open-source, Java library that contains facilities and algorithms for common but difficult to implement tasks such as reading, writing, searching, merging, comparing and transforming pathway information |
Payao |
Payao is a community platform for SBML pathway model curation |
PBSK browser |
PBSK browser allows users to navigate biological pathways of PSI-MI, BioPAX, SBML and KGML formats |
PDB |
An Information Portal to Biological Macromolecular Structures |
PDBe |
The Protein Data Bank in Europe (PDBe) is bringing structure to biology |
PDDB |
Prion Disease Database (PDDB) focuses on data used in Prion Disease (PD) research This site provides tools which allow scientists to analyze, store, and share this PD data with other scientists |
PEANuT |
Pathway enrichment analysis tool provides an up-front method to identify underlying biological principles by calculating enriched pathways in focus networks |
PENTACON |
The Personalized NSAID Therapeutics Consortium (PENTACON) is a group of scientists with a wide range of expertise from multiple institutions whose collective aim is to develop a paradigm for the personalization of drug treatment |
PharmGKB |
Integrated data resource about how variation in human genetics leads to variation in response to drugs |
PhosphoELM |
PhosphoELM is a database of phosphorylation sites - Update 2008 |
PIG |
Pathogen Interaction Gateway is a database of host-pathogen PPI (HP-PPI) data from a number of public resources |
PIR |
Protein Information Resource (PIR) is an integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies |
PlantReactome |
A freely accessible plant pathway database which hosts plant metabolic and regulatory pathways |
PLAZA |
A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants |
PolyDoms |
PolyDoms is a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease |
Pomelo II |
Pomelo II is an open-source, web-based, freely available tool for the analysis of gene (and protein) expression and tissue array data |
PosMed |
Positional MEDLINE (PosMed) prioritizes candidate genes for positional cloning |
PpiTrim |
PpiTrim is for constructing non-redundant and up-to-date interactomes |
Predicted Arabidopsis Interactome Resource |
A database of potential plant interactions, detailed annotations and more specific per interaction confidence measurement |
PRGdb |
PRGdb is a community-based database model for the analysis of R-genes in plants |
PRIDE |
The Proteomics Identifications database at EBI is a mass spectrometry-derived proteomics data repository |
Prioritizer |
A prioritization method for positional candidate genes, by assuming that the majority of causative genes are functionally closely related |
PRO |
Protein Ontology (PRO) is a formal representation of protein objects, providing both descriptions of these objects and the relationships between them |
PROGgeneV2 |
PROGgeneV2 is a Pan Cancer Prognostics Database |
ProKinO |
ProKinO is a framework for protein kinase ontology |
Proteomic |
Proteomic atlas of the human olfactory bulb |
PSI-MI |
The HUPO Proteomics Standards Initiative Molecular Interaction (PSI-MI) workgroup defines community standards for data representation in proteomics to facilitate data comparison, exchange and verification |
PSIQUIC |
PSIQUIC a web service to access the PSI-MI interaction data |
pSTIING |
pSTIING is a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer |
PUPPI |
PUPPI is a pathway analysis method using protein-protein interaction network for case-control data |
PyBioS |
PyBioS is a system for the modeling and simulation of cellular processes |
Quartz-Seq |
Quartz-Seq is a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity |
RDF2Graph |
RDF2Graph a tool to recover, understand and validate the ontology of an RDF resource |
RDFScape |
RDFScape is a plugin that has been developed to to query, visualize and reason on ontologies represented in OWL or RDF within Cytoscape |
Reactome.db |
A set of annotation maps for reactome assembled using data from Reactome |
ReactomePA |
ReactomePA is a R package for Reactome Pathway Analysis |
ReConn |
ReConn is a Java plugin that connects Cytoscape to the Reactome database |
RefNetBuilder |
RefNetBuilder is a platform for construction of integrated reference gene regulatory networks from expressed sequence tags |
Regulatory Genomics |
A Database of Annotated Promoters of Genes Associated with Common Respiratory and Related Diseases |
ReMatch |
ReMatch is a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis |
REPAIRtoire |
REPAIRtoire is a database of DNA repair pathways |
RGD |
Rat Genome Database (RGD) is a collection of genetic and genomic information on the rat |
Rhea |
Rhea is a manually curated resource of biochemical reactions |
RhesusBase |
RhesusBase is a knowledgebase for the monkey research community |
RMOD |
A Tool for Regulatory Motif Detection in Signaling Network |
RNApathwaysDB |
RNApathwaysDB is a database of RNA maturation and decay pathways |
ROCK |
ROCK is a breast cancer functional genomics resource |
Rspider |
R spider is a web-based tool for the analysis of a gene list using the systematic knowledge of core pathways and reactions in human biology accumulated in the REACTOME and KEGG databases |
RxnFinder |
RxnFinder is a Biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity |
SABIO-RK |
System for the Analysis of Biochemical Pathways - Reaction Kinetics is a web-based application based on the SABIO relational database that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured |
SAGA |
SAGA is a subgraph matching tool for biological graphs |
SASD |
Synthetic Alternative Splicing Database for identifying novel isoform from proteomics |
SASD |
SASD is the Synthetic Alternative Splicing Database for identifying novel isoform from proteomics |
SB-KOM |
SB-KOM provides integration of pathway information using BioPax |
SBGN |
Systems Biology Graphical Notation (SBGN) project is an effort to standardize the graphical notation used in maps of biological processes |
SBKD |
The Structural Biology Knowledgebase is a portal to protein structures, sequences, functions, and methods |
SBML |
The Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biological processes |
SBML-Bridge |
SBML-Bridge is an XML Pathway Converting Tool |
SciMiner |
SciMiner is a dictionary- and rule-based biomedical literature mining and functional enrichment analysis tool |
SIDEKICK |
SIDEKICK is a genomic data driven analys is and decision-making framework |
SigCS |
An integrated genetic information resource for human cerebral stroke |
SignaLink |
SignaLink allows system-level analyses using the network of the major intracellular signaling pathways |
Signalogs |
Signalogs is an Orthology-based identification of novel signaling pathway components in three metazoans |
SignS |
SignS is a web tool for gene selection and signature finding in problems where the dependent variable is patient survival or, more generally, a right-censored variable |
SimBiology 3.1 |
SimBiology¬ provides graphical and programmatic tools for computational systems biology and pharmacokinetics |
SIPPER |
SIPPER is a flexible method to integrate heterogeneous data into a metabolic network |
SMART |
SMART displays domains in the context of genomes and networks |
SMPDB |
The Small Molecule Pathway Database (SMPDB) is an interactive, visual database containing more than 350 small-molecule pathways found in humans |
SNPranker |
SNPranker is a gene-centric data mining tool for diseases associated SNP prioritization in GWAS |
SOURCE |
SOURCE is a unification tool which dynamically collects and compiles data from many scientific databases, and thereby attempts to encapsulate the genetics and molecular biology of genes from the genomes of Homo sapiens, Mus musculus, Rattus norvegicus into easy to navigate GeneReports |
SPARQLGraph |
SPARQLGraph is a web-based platform for graphically querying biological Semantic Web databases |
SPIKE |
Signaling Pathway Integrated Knowledge Engine is an interactive software environment that graphically displays biological signaling networks, allows dynamic layout and navigation through these networks, and enables the superposition of DNA microarray and other functional genomics data on interaction maps |
SPIRE |
SPIRE is a Systematic protein investigative research environment |
StarBase |
StarBase will decode miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data |
STITCH |
STITCH is an interaction network database for small molecules and proteins |
STRING |
STRING is global view on proteins and their functional interactions in 630 organisms |
SuperTarget |
SuperTarget is an on drug-target interactions resource |
SyBiL |
Systems Biology Linker is designed for visualizing pathway data files in BioPAX format, such as imported from Reactome and converting BioPAX file into SBML file |
SZGR |
SZGR is a comprehensive schizophrenia gene resource |
T1DBase |
T1DBase focuses on two research areas in type 1 diabetes (T1D) and the genetics of T1D susceptibility and beta cell biology |
T2D-Db |
T2D-Db is a database of all molecular factors reported to be involved in the pathogenesis of Type 2 diabetes in human, mouse and rat |
T2D@ZJU |
T2D@ZJU is a knowledgebase integrating heterogeneous connections associated with type 2 diabetes mellitus |
T2DM-GeneMiner |
T2DM-GeneMiner is a web resource for analysing genes in relation to type 2 diabetes mellitus |
Taverna |
Taverna Workbench is an open source tool for designing and executing workflows created by the myGrid project |
TcoF-DB |
TcoF-DB is provide a comprehensive starting point for investigations into transcriptional regulation that include PPIs between Transcription Factors, Transcription Co-factors and other proteins |
TEAK |
TEAK is a Topology Enrichment Analysis frameworK for detecting activated biological subpathways |
The Cell Collective |
The Cell Collective is an open and collaborative approach to systems biology |
The Cell Cycle Ontology |
The Cell Cycle Ontology is an application ontology that automatically captures and integrates detailed knowledge on the cell cycle process |
TIM |
TIM (Tools to Input Models) is a tool which integrates biological objects and information about biological process modelling |
Toppgene |
Toppgene Suite is an one-stop portal for gene list enrichment analysis and candidate gene prioritization based on functional annotations and protein interactions network |
TranscriptomeBrowser |
TranscriptomeBrowser is introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks |
TransDomain |
TransDomain is a transitive domain-based method in protein-protein interaction prediction |
TRANSPATH |
TRANSPATH is an information resource for storing and visualizing signaling pathways and their pathological aberrations |
tYNA platform |
The tYNA platform for comparative interactomics is a web tool for managing, comparing and mining multiple networks |
UCD 2D-PAGE Database |
UCD 2D-PAGE Datavase is a Two-dimensional polyacrylamide gel electrophoresis database |
UCSC Genome Browser |
UCSC Genome Browser is an up-to-date source for genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations |
UCSD-Nature Signaling Gateway |
The UCSD-Nature Signaling Gateway is a comprehensive and up-to-the-minute resource for anyone interested in signal transduction |
UniHI |
The Unified Human Interactome database provides researchers with a comprehensive platform to query and access human protein-protein interaction (PPI) data |
UniProtKB |
The UniProt Knowledgebase is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation |
VANTED |
Visualization and Analysis of Networks containing Experimental Data makes it possible to load and edit graphs, which may represent biological pathways or functional hierarchies |
varSelRF |
varSelRF is a R package for gene selection and classification using random forest |
VeryGene |
VeryGene serves as a tissue-specific genes knowledgebase and a discovery tool to generate testable hypotheses for basic and clinical research |
viPEr |
Virtual pathway explorer is a cytoscape app, which integrates _omics data with interactome data |
VirHostNet |
VirHostNet (Virus-Host Network) is a knowledgebase system dedicated to the curation, the integration, the management and the analysis of virus-host molecular (mainly protein-protein) interaction networks as well as their functional annotation (molecular functions, cellular pathways, protein domains) |
visANT |
visANT is an integrative visual analysis tool for biologucal networjs and pathways |
VisHiC |
VisHiC is a public web server for clustering and interpreting gene expression data |
Voronto |
Voronto is a Mapper for expression data to ontologies |
WAVe |
WAVe is a web analysis of the variome |
Web Apollo |
Web Apollo is a web-based genomic annotation editing platform |
WhichGenes |
WhichGenes is a web-based interactive gene set building tool offering a very simple interface to extract always-updated gene lists from multiple databases and unstructured biological data sources |
Wiki-Pi |
A Web-Server of Annotated Human Protein-Protein Interactions to Aid in Discovery of Protein Function |
WikiCell |
WikiCell is a unified resource platform for human transcriptomics research |
WikiPathways |
WikiPathways is an open, public platform dedicated to the curation of biological pathways by and for the scientific community |
WIM |
WIM (Web Interfac for Modelling) is a tool which integrates biological objects and information about biological process modelling |
WormBase |
WormBase is a central data repository for nematode biology |
YMDB |
YMDB is a yeast metabolome database |
yOWL |
yOWL represent knowledge found in the Saccharomyces Genomes Database using OWL (Web Ontology Language). |