Metabolic network data | Pathway analysis

Metabolic pathways are series of enzymatic reactions that convert an initial substrate to the final end-products and are connected by their intermediates.

HRGRN
Data

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…

MEMOSys
Data

MEMOSys MEtabolic MOdel research and development System

A versatile database for the management, storage and development of…

A versatile database for the management, storage and development of genome-scale models (GEMs). Since its initial release, the database has undergone major improvements, and the new version…

PathCaseMAW
Web

PathCaseMAW PathCase Metabolomics Analysis Workbench

Provides a database-enabled framework and Web-based computational tools for…

Provides a database-enabled framework and Web-based computational tools for browsing, querying, analyzing and visualizing stored metabolic networks. PathCaseMAW is easy to work with by design, and is…

BiGG Models
Data

BiGG Models

A completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG…

A completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scale metabolic models. On the website, users can…

ReconMap
Web
Desktop

ReconMap

A comprehensive curated map of human metabolism presented utilizing the Google…

A comprehensive curated map of human metabolism presented utilizing the Google Maps application program interface (API) for highly responsive interactive navigation within a platform that facilitates…

YeastCyc
Data

YeastCyc

A Pathway/Genome Database of the model eukaryote Saccharomyces cerevisiae…

A Pathway/Genome Database of the model eukaryote Saccharomyces cerevisiae S288c. YeastCyc contains, in addition to genomic information, metabolic pathway, reaction, enzyme, and compound information,…

Plant Reactome
Data

Plant Reactome

A network of plant proteins linked to their molecular functions and interactors…

A network of plant proteins linked to their molecular functions and interactors in the context of their locations within the plant cell. Plant Reactome provides intuitive bioinformatics tools for the…

BioNetGen
Desktop

BioNetGen

An open-source package for the specification and simulation of rule-based…

An open-source package for the specification and simulation of rule-based models of biochemical systems, including signal transduction, metabolic, and genetic regulatory networks. BioNetGen has been…

FUNGIpath
Data

FUNGIpath

A tool built using a two-stage approach. Groups of orthologous proteins…

A tool built using a two-stage approach. Groups of orthologous proteins predicted using complementary methods of detection were collected in a relational database. Each group was further mapped on to…

FragariaCyc
Data

FragariaCyc

A strawberry-specific cellular metabolic network based on the annotated genome…

A strawberry-specific cellular metabolic network based on the annotated genome sequence of Fragaria vesca L. ssp. vesca, accession Hawaii 4. FragariaCyc was built on the Pathway-Tools platform using…

ArthropodaCyc
Data

ArthropodaCyc

A collection of databases dedicated to the arthropod metabolism reconstruction.…

A collection of databases dedicated to the arthropod metabolism reconstruction. ArthropodaCyc allows researchers to perform reliable metabolism comparisons of fully sequenced arthropods genomes.…

MetaNetX
Data

MetaNetX

A repository of genome-scale metabolic networks (GSMNs) and biochemical…

A repository of genome-scale metabolic networks (GSMNs) and biochemical pathways from a number of major resources imported into a common namespace of chemical compounds, reactions, cellular…

Cell ML Tools
Format

Cell ML Tools

An open standard based on the XML markup language. The purpose of CellML is to…

An open standard based on the XML markup language. The purpose of CellML is to store and exchange computer-based mathematical models. CellML allows scientists to share models even if they are using…

DESM
Data

DESM

A platform for discovery, analysis and exploration of information from a number…

A platform for discovery, analysis and exploration of information from a number of topic-specific microbial knowledgebases. The knowledgebases include integrated information from published scientific…

KEGG
Data

KEGG

An integrated database resource consisting of 16 main databases, which are…

An integrated database resource consisting of 16 main databases, which are categorized into systems, genomic, chemical and health information. The PATHWAY, BRITE and MODULE databases in the systems…

kpath
Data

kpath

Integrates information related to metabolic pathways. kpath also provides a…

Integrates information related to metabolic pathways. kpath also provides a navigational interface that enables not only the browsing, but also the deep use of the integrated data to build metabolic…

LmTDRM
Data

LmTDRM Thiol Disulphide Redox Metabolic

A comprehensive web-based database on thiol proteins and their functions. It…

A comprehensive web-based database on thiol proteins and their functions. It includes: Description, Search, TDRM analysis, and genome viewer. The quality of these data has been evaluated before they…

M-path
Web

M-path

A computational platform, M-path, to explore synthetic metabolic pathways…

A computational platform, M-path, to explore synthetic metabolic pathways including putative enzymatic reactions and compounds. M-path is an iterative random algorithm which makes efficient use of…

MetRxn
Data

MetRxn

A knowledgebase that includes standardized metabolite and reaction descriptions…

A knowledgebase that includes standardized metabolite and reaction descriptions by integrating information from BRENDA, KEGG, MetaCyc, Reactome.org and 44 metabolic models into a single unified data…

LeishCyc
Data

LeishCyc

Describes Leishmania major genes, gene products, metabolites, their…

Describes Leishmania major genes, gene products, metabolites, their relationships and biochemical organization into metabolic pathways. LeishCyc provides a systematic approach to organizing the…

TrypanoCyc
Data

TrypanoCyc

A dynamic database which describes the generic and condition-specific metabolic…

A dynamic database which describes the generic and condition-specific metabolic network of Trypanosoma brucei, a parasitic protozoan responsible for human and animal African trypanosomiasis. In…

metabolicMine
Data

metabolicMine

Integrates data sets from a range of experiments and model organisms alongside…

Integrates data sets from a range of experiments and model organisms alongside tools for exploring them. The current version brings together information covering genes, proteins, orthologues,…

SFGD
Data

SFGD Soybean Functional Genomics Database

A comprehensive database integrating genome and transcriptome data, and also…

A comprehensive database integrating genome and transcriptome data, and also for soybean acyl-lipid metabolism pathways. SFGD provides useful toolboxes for biologists to improve the accuracy and…

SABIO-RK
Web

SABIO-RK

A curated database that contains information about biochemical reactions, their…

A curated database that contains information about biochemical reactions, their kinetic rate equations with parameters and experimental conditions. All the data are manually curated and annotated by…

SubtiWiki
Data

SubtiWiki

A free collaborative resource for the Bacillus community. It is based on the…

A free collaborative resource for the Bacillus community. It is based on the idea that a community of experts that produces new knowledge every day is the best suited group for keeping a data…

ProcessDB
Data

ProcessDB

Helps molecular cell biologists manage and test their increasingly complex…

Helps molecular cell biologists manage and test their increasingly complex mechanistic hypotheses. ProcessDB does this with a graphical user interface that helps users formulate, visualize, compare,…

PMAP
Data

PMAP Proteolysis MAP

A user-friendly website intended to aid the scientific community in reasoning…

A user-friendly website intended to aid the scientific community in reasoning about proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. The…

Reactome
Data

Reactome

Provides molecular details of signal transduction, transport, DNA replication,…

Provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular transformations—an extended version of a…

RiceCyc
Data

RiceCyc

A catalog of known and/or predicted biochemical pathways from rice (Oryza…

A catalog of known and/or predicted biochemical pathways from rice (Oryza sativa). Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene database…

PATIKA
Data

PATIKA Pathway Analysis Tools for Integration and Knowledge Acquisition

It is composed of a server-side, scalable, object-oriented database and…

It is composed of a server-side, scalable, object-oriented database and client-side editors to provide an integrated, multi-user environment for visualizing and manipulating network of cellular…

PAGED
Data

PAGED Pathway And Gene Enrichment Database

Enables comprehensive searches for disease-specific pathways, gene signatures,…

Enables comprehensive searches for disease-specific pathways, gene signatures, microRNA targets, and network modules by integrating gene-set-based prior knowledge as molecular patterns from multiple…

Pathway Commons
Data

Pathway Commons

Enables biologists to browse and search a comprehensive collection of pathways…

Enables biologists to browse and search a comprehensive collection of pathways from multiple sources represented in a common language, the BioPAX format. Data providers can share their pathway data…

PeroxisomeDB
Data

PeroxisomeDB Peroxisome DataBase

Aims to organise and integrate curated information on peroxisomal genes, their…

Aims to organise and integrate curated information on peroxisomal genes, their encoded proteins, their molecular function and metabolic pathway they belong to, and their related disorders. Additional…

PMN
Data

PMN Plant Metabolic Network

Metabolic networks reconstructed from sequenced genomes or transcriptomes can…

Metabolic networks reconstructed from sequenced genomes or transcriptomes can help visualize and analyze large-scale experimental data, predict metabolic phenotypes, discover enzymes, engineer…

IUBMB-Nicholson…
Data

IUBMB-Nicholson maps

A collection of metabolic pathway diagrams curated by Donald Nicholson at the…

A collection of metabolic pathway diagrams curated by Donald Nicholson at the University of Leeds, England.

Nematode.net
Data

Nematode.net

Disseminates diverse bioinformatic data sets and provide analysis tools to the…

Disseminates diverse bioinformatic data sets and provide analysis tools to the broad scientific community in a useful and user-friendly manner. Next-generation data has been added to the various…

MouseCyc
Data

MouseCyc

Linking biochemical genetic data to the reference genome for the laboratory…

Linking biochemical genetic data to the reference genome for the laboratory mouse is important for comparative physiology and for developing mouse models of human biology and disease. MouseCyc is a…

NCBI BioSystems
Data

NCBI BioSystems

Provides integrated access to biological systems and their component genes,…

Provides integrated access to biological systems and their component genes, proteins, and small molecules, as well as literature describing those biosystems and other related data throughout Entrez.…

MetNetDB
Data

MetNetDB MetNet database

Contains information on networks of metabolic and regulatory and interactions…

Contains information on networks of metabolic and regulatory and interactions in Arabidopsis. This information is based on input from biologists in their area of expertise. In addition to the…

MODOMICS
Data

MODOMICS

A database of RNA modifications that provides comprehensive information…

A database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides, their biosynthetic pathways, RNA-modifying enzymes and location…

MMMDB
Data

MMMDB Mouse Multiple tissue Metabolome DataBase

Provides comprehensive and quantitative metabolomic information for multiple…

Provides comprehensive and quantitative metabolomic information for multiple tissues from single mice. MMMDB is designed to normalize users' data, which can be submitted online and used to…

RNApathwaysDB
Data

RNApathwaysDB

Contains components involved in the RNA metabolic pathways of three main RNA…

Contains components involved in the RNA metabolic pathways of three main RNA classes (mRNA, tRNA and rRNA). RNApathwaysDB can be queried with keywords, and sequences of protein enzymes involved in…

LAMP
Data

LAMP Library of Apicomplexan Metabolic Pathways

A web database that provides near complete mapping from genes to the central…

A web database that provides near complete mapping from genes to the central metabolic functions for some of the prominent intracellular parasites of the phylum Apicomplexa. This phylum includes the…

MaizeCyc
Data

MaizeCyc

A catalog of known and/or predicted metabolic and transport pathways from maize…

A catalog of known and/or predicted metabolic and transport pathways from maize (Zea mays ssp. mays). Pathways and genes presented in this catalog are based on the electronic and manual annotations…

Malaria…
Data

Malaria Parasite Metabolic Pathways

The genome project of Plasmodium falciparum has been completed and other…

The genome project of Plasmodium falciparum has been completed and other plasmodia species are on the line. The metabolic pathways of Plasmodium were extracted from the Kyoto University Encyclopedia…

MedicCyc
Data

MedicCyc

A biochemical pathway database for Medicago truncatula. MedicCyc was assembled…

A biochemical pathway database for Medicago truncatula. MedicCyc was assembled based on new genomic sequence data and over 225,000 Medicago truncatula ESTs. The initial compilation was manually…

MetaCyc
Web

MetaCyc

A comprehensive and freely accessible database describing metabolic pathways…

A comprehensive and freely accessible database describing metabolic pathways and enzymes from all domains of life. MetaCyc pathways are experimentally determined, mostly small-molecule metabolic…

metaTIGER
Web

metaTIGER

It has been created, using genomic information from 121 eukaryotes and 404…

It has been created, using genomic information from 121 eukaryotes and 404 prokaryotes and sensitive sequence search techniques to predict the presence of metabolic enzymes. These enzyme sequences…

IPAD
Web

IPAD Integrated Pathway Analysis Database

A comprehensive database covering about 22,498 genes, 25,469 proteins, 1956…

A comprehensive database covering about 22,498 genes, 25,469 proteins, 1956 pathways, 6704 diseases, 5615 diseases, and 52 organs integrated from databases including the BioCarta, KEGG, NCI-Nature…

iPAVS
Web

iPAVS integrated Pathway resources, Analysis and Visualization System

An integrated biological pathway database designed to support pathway discovery…

An integrated biological pathway database designed to support pathway discovery in the fields of proteomics, transcriptomics, metabolomics and systems biology. The key goal of IPAVS is to provide…

IntPath
Web

IntPath

A pathway gene relationship database that integrates data from KEGG,…

A pathway gene relationship database that integrates data from KEGG, WikiPathways, BioCyc. Currently, the following organisms are included: Homo sapiens, Mus musculus, Saccharomyces cerevisiae and…

KaPPA-View
Data

KaPPA-View

A metabolic pathway database which is able to overlay gene-to-gene and/or…

A metabolic pathway database which is able to overlay gene-to-gene and/or metabolite-to-metabolite relationships as curves on a metabolic pathway map, or on a combination of up to four maps. This…

hiPathDB
Data

hiPathDB

An integrated pathway database that combines the curated human pathway data of…

An integrated pathway database that combines the curated human pathway data of NCI-Nature PID, Reactome, BioCarta and KEGG. hiPathDB provides two different types of integration. The pathway-level…

HPD
Web

HPD Human Pathway Database

Developed the by integrating heterogeneous human pathway data that are either…

Developed the by integrating heterogeneous human pathway data that are either curated at the NCI Pathway Interaction Database (PID), Reactome, BioCarta, KEGG or indexed from the Protein Lounge Web…

HumanCyc
Data

HumanCyc

Provides a genome-based view of human nutrition that associates the essential…

Provides a genome-based view of human nutrition that associates the essential dietary requirements of humans with a set of metabolic pathways whose existence is supported by the human genome. The…

IMID
Data

IMID Integrated Molecular Interaction Database

Molecular interaction information can be searched using the search function…

Molecular interaction information can be searched using the search function below, where you may enter specific keywords according to your search criteria. You can limit your search by pathways,…

ECMDB
Data

ECMDB EColi Metabolome DataBase

An expertly curated database containing extensive metabolomic data and…

An expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655). This database includes significant quantities of…

FlyReactome
Data

FlyReactome

A curated repository for Drosophila melanogaster pathways and reactions. The…

A curated repository for Drosophila melanogaster pathways and reactions. The information in this database is authored by biological researchers with expertise in their fields, maintained by the…

CathaCyc
Data

CathaCyc

A detailed metabolic pathway database, from C. roseus RNA-Seq data sets.…

A detailed metabolic pathway database, from C. roseus RNA-Seq data sets. CathaCyc contains 390 pathways with 1,347 assigned enzymes and spans primary and secondary metabolism. Curation of the…

BioCyc
Data

BioCyc

A collection of 5500 Pathway/Genome Databases (PGDBs), plus software tools for…

A collection of 5500 Pathway/Genome Databases (PGDBs), plus software tools for understanding their data. BioCyc provides tools for navigating, visualizing, and analyzing the underlying databases, and…

BioPath
Data

BioPath

A database of biochemical pathways that provides access to metabolic…

A database of biochemical pathways that provides access to metabolic transformations and cellular regulations derived from the Roche Applied Science "Biochemical Pathways" wall chart. In…

Biozon
Data

Biozon

A unified biological database that integrates heterogeneous data types such as…

A unified biological database that integrates heterogeneous data types such as proteins, structures, domain families, protein-protein interactions and cellular pathways, and establishes the…

AHD
Data

AHD Arabidopsis Hormone Database

A collection of hormone related genes of the model organism Arabidopsis…

A collection of hormone related genes of the model organism Arabidopsis thaliana. You can find useful information on eight major phytohormones: abscisic acid, auxin, brassinosteroid, cytokinin,…

Arabidopsis…
Data

Arabidopsis Reactome

A knowledgebase of biological processes in Arabidopsis. It covers biological…

A knowledgebase of biological processes in Arabidopsis. It covers biological pathways ranging from the basic processes of metabolism to high-level processes such as cell cycle regulation. While…

AtIPD
Data

AtIPD Arabidopsis thaliana Isoprenoid Pathway Database

Provides access to manually curated list of Arabidopsis isoprenoid pathways and…

Provides access to manually curated list of Arabidopsis isoprenoid pathways and genes, and allows to visualize pathway topology. The database was compiled using information on pathways and pathway…

AraCyc
Data

AraCyc

Contains biochemical pathways of Arabidopsis, developed at The Arabidopsis…

Contains biochemical pathways of Arabidopsis, developed at The Arabidopsis Information Resource. The aim of AraCyc is to represent Arabidopsis metabolism as completely as possible with a…

BESC…
Data

BESC Knowledgebase

Serves as a centralized repository for experimentally generated data and to…

Serves as a centralized repository for experimentally generated data and to provide an integrated, interactive and user-friendly analysis framework. The Portal makes available tools for…

Recon2Neo4j
Desktop

Recon2Neo4j

Facilitates exploration of highly-connected and comprehensive human metabolic…

Facilitates exploration of highly-connected and comprehensive human metabolic data and identification of metabolic subnetworks of interest. Recon2Neo4j provides two major components: i) a graph…

MRAD
Data

MRAD Metabolic Reaction Analysis Database

A relational database based on the entity-relationship (ER) model which…

A relational database based on the entity-relationship (ER) model which combines information about organisms, biochemical pathways, reactions, enzymes, substrates, products and genes. MRAD describes…

Plantmetabolomi…
Data

Plantmetabolomics.org

Contains comprehensive targeted and untargeted mass spectrum metabolomics data…

Contains comprehensive targeted and untargeted mass spectrum metabolomics data for Arabidopsis mutants across a variety of metabolomics platforms. The database allows users to generate hypotheses…

BIOBASE…
Data

BIOBASE PROTEOME

A knowledgebase containing data on genes and miRNAs, the diseases they are…

A knowledgebase containing data on genes and miRNAs, the diseases they are associated with, the drugs they are targeted by, and the pathways and networks they act within. Based on its extensive…

MetaCrop
Data

MetaCrop

A manually curated repository of high-quality data about plant metabolism,…

A manually curated repository of high-quality data about plant metabolism, providing different levels of detail from overview maps of primary metabolism to kinetic data of enzymes. MetaCrop contains…

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