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ASIAN -- a web server for inferring a regulatory network framework from gene expression profiles
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| Infer a framework of regulatory networks from a large number of gene expression profiles. |
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AVIS -- AJAX viewer of interactive signaling networks
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| A web-based viewer of interactive cell signaling networks.
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Ambion GeneAssist™ Pathway Atlas
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| Learn how a protein is involved in different cellular pathways.
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BIND -- The Biomolecular Interaction Network Database
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| Find biomolecular interaction, complex and pathway information.
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BioCarta -- Online maps of metabolic and signaling pathways
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| Search extensive collection of dynamic maps of classic metabolic and signal transduction pathway maps.
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BioGRID -- a general repository for interaction datasets
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| Developed to house and distribute collections of protein and genetic interactions from major model organism species.
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BiologicalNetworks -- visualization and analysis tool for systems biology
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| Construct, retrieve, analyze and visualize various types of biological networks.
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CCDB -- Cell Cycle Database
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| A biological resource that collects the most relevant information related to genes and proteins involved in human and yeast cell cycle processes.
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CYCLONET — an integrated database on cell cycle regulation and carcinogenesis
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| Search information on cell cycle regulation in mammals in normal and pathological states
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CellCircuits -- a database of protein network models
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| Search for information on molecular network models.
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Cyclebase.org -- a comprehensive multi-organism online database of cell-cycle experiments
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| Search a centralized database containing data from a large number of cell-cycle microarray studies.
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DAVID -- A Database for Annotation, Visualization and Integrated Discovery
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| Conduct comprehensive gene annotation, expression data analysis, biological pathway mapping, and other functional genomics tasks.
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DAVID Knowledgebase -- a backend database used for all DAVID bioinformatics tools
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| A gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis.
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DRASTIC—INSIGHTS -- querying information in a plant gene expression database
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| Search for information of plant gene expression in response to pathogens and environmental changes. |
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EndoNet -- an information resource about regulatory networks of cell-to-cell communication
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| Search for information about intercellular regulatory communication.
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GenMAPP--Gene Microarray Pathway Profiler
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| Visualize and analyze gene expression data in the context of biological pathways. |
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GeneNet -- A database on structure and functional organization of gene networks
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| Search for information on gene networks, such as metabolic pathways and signal transduction pathways.
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GenePath -- from mutations to genetic networks and back
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| Analyze mutant-based experiments and synthesize genetic networks.
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GraphWeb -- graph-based analysis of biological networks
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| Mining heterogeneous biological networks for gene modules with functional significance.
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HPMR Human plasma membrane receptome -- sequences, literature, and expression data
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| Search for comprehensive information on Human plasma membrane receptome. |
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Hedgehog Signaling Pathway Database -- a repository of current annotation efforts and resources for the Hh research community
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| Search for comprehensive information on the Hedgehog developmental pathways and Hedgehog research..
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IntAct -- An Open Source Molecular Interaction Database
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| Search and analyze protein interactions. |
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KEGG BRITE Database
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| Map genomic and molecular data to biological systems and functions.
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KEGG PATHWAY Database
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| Search a collection of pathway maps on metabolism, signal transduction, gene regulation, and cellular processes. |
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KOBAS server -- a web-based platform for automated annotation and pathway identification
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| Annotate a set of nucleotide or protein sequences with KEGG Orthology terms and identify frequently occurring or statistically significantly enriched pathways among the queried sequences.
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MiST -- a microbial signal transduction database
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| Search for information on signal transduction proteins from 459 complete bacterial and archaeal organisms.
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NCI/Nature Pathway Interaction Database
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| A collection of curated and peer-reviewed pathways composed of human molecular signaling and regulatory events and key cellular processes. |
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NET-SYNTHESIS -- a software for synthesis, inference and simplification of signal transduction networks
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| A software for combined synthesis, inference and simplification of signal transduction networks.
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NeAT -- network analysis tools
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| A toolbox for the analysis of biological networks, clusters, classes and pathways.
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PANTHER -- A browsable database of gene products organized by biological function, using curated protein family and subfamily classification
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| Browse and search proteins based on their biological functions. |
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PHOSIDA -- Phosphorylation site database
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| Search for phosphorylation data of any protein of interest. |
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Pathguide -- a pathway resource list
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| Search for database and tools relevant to biological pathway study from this comprehensive resources list. |
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PathoPlant® -- a platform for microarray expression data to analyze co-regulated genes involved in plant defense responses
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| Search for information on plant-pathogen interactions, signal transduction, and microarray gene expression during plant pathogenesis. |
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PathwayExplorer -- web service for visualizing high-throughput expression data on biological pathways
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| Visualize high-throughput microarray gene expression data on biological pathways. |
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PhosphoPOINT -- a comprehensive human kinase interactome and phospho-protein database
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| Uncover novel substrates for specific kinases.
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PhosphoSite -- A bioinformatics resource dedicated to physiological protein phosphorylation.
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| Search the database of in vivo phosphorylation sites of human and mouse proteins
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Prediction of lipid posttranslational modifications and localization signals from protein sequences -- big-Pi, NMT and PTS1.
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| Predict lipid posttranslational modifications and localization signals from protein sequences. |
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ProdoNet -- identification and visualization of prokaryotic gene regulatory and metabolic networks
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| Application for the mapping of prokaryotic genes and the corresponding proteins to common gene regulatory and metabolic networks.
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ROSPath -- ROS-mediated cell signaling pathway information repository
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| Search for information pertaining to signaling mediated through reactive oxygen species.
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Reactome -- a curated knowledgebase of biological pathways
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| Find comprehensive biological pathway information from a curated resource of core pathways and reactions in human biology.
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SENTRA -- A Database of Signal Transduction Proteins for Prokaryotes
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| Search for annotated sequence information of prokaryotic signal transduction proteins. |
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STCDB -- Signal Transduction Classification Database
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| Search for information on the classification of signal transduction in eukaryotic cells.
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ScanSite 2.0 -- Proteome-wide prediction of cell signaling interactions using short sequence motifs
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| Search for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or PDZ domains. |
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Science STKE Literature
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| Find perspectives, reviews, protocols and journal articles focused on cell signaling. |
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T-REGs -- A list of TGFbeta-responsive genes
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| Search for information on TGFbeta responsive genes. |
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TRANSPATH ® -- An integrated database on signal transduction and a tool for array analysis
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| Analyze and visualize gene regulatory networks that combines encyclopedic information on signal transduction pathway.
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The Molecule Pages database
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| Provides essential information on more than 3800 mammalian proteins involved in cellular signaling.
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The aMAZE LightBench -- A Relational Database of Cellular Processes
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| Search for information on metabolic and regulatory pathways.
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VisANT -- Integrative Visual Analysis Tool for Biological Networks and Pathways
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| Tool for pathway visualization, editing, prediction and construction.
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Wnt Database
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| Search for comprehensive information on Wnt proteins and Wnt signaling pathways. |
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pSTIING -- a ‘systems’ approach towards integrating signaling pathways, interaction and transcriptional regulatory networks in inflammation and cancer
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| Search for comprehensive knowledge about protein-protein, protein-lipid, protein-small molecules, ligand-receptor interactions, receptor-cell type information, transcriptional regulatory and signal transduction modules relevant to inflammation, cell migration and tumourigenesis. |
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