Biochemical and metabolic pathways
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AraCyc: Arabidopsis thaliana Biochemical Pathways
AraCyc: Arabidopsis thaliana Biochemical Pathways. Main Query Page. The main query page for searching Pathways, Genes, Enzymes, Compounds and more. Metabolic Map. A 'bird's eye' view of Arabidopsis metabolism.
BioCarta
MAIN CATEGORIES Observe how genes interact in dynamic graphical models. Our online maps depict molecular relationships from areas of active research. In an "open source" approach, this community-fed forum constantly integrates emerging ...
BioCyc
BioCyc collection of 250+ Pathway/Genome Databases.
Includes the extensively curated MetaCyc multiorganism metabolic pathway and enzyme database, the EcoCyc database for Escherichia coli
K-12, and the HumanCyc database of human metabolic pathways.
BioPathways Consortium
The mission of the BioPathways Consortium is to catalyze the emergence and development of computational pathways biology, by building up a strong and coherent scientific community, sharing knowledge, facilitating collaborations, and fostering the development of methods and tools of wide interest to the community.
KEGG
Kyoto Encyclopedia of Genes and Genomes (deciphering the genome). A grand challenge in the post-genomic era is a complete computer representation of the cell and the organism, which will enable computational prediction of higher-level complexity of cellular processes and organism behavior from genomic information. Toward this end we have been developing a knowledge-based approach for network prediction, which is to predict, given a complete set of genes in the genome, the protein interaction networks that are responsible for various cellular processes. KEGG at is the reference knowledge base that integrates current knowledge on molecular interaction networks such as pathways and complexes (PATHWAY database), information about genes and proteins generated by genome projects (GENES/SSDB/KO databases) and information about biochemical compounds and reactions (COMPOUND/GLYCAN/REACTION databases). These three types of database actually represent three graph objects, called the protein network, the gene universe and the chemical universe. New efforts are being made to abstract knowledge, both computationally and manually, about ortholog clusters in the KO (KEGG Orthology) database, and to collect and analyze carbohydrate structures in the GLYCAN database.
PFBP
Protein Function and Biochemical Pathways (PFBP) Project. The goal of the PFBP project is to develop a comprehensive resource (aMAZE database) containing information on organism and tissue specific metabolic, and later other biochemical pathways that can be queried more flexibly than other existing resources and extended to include proprietary data. This database is to re-cast information contained in the enzyme function databank BRENDA, which includes details on the enzymatic reactions, substrates and products, binding and catalytic constants as well as a rich collection of literature references for nearly all the enzymes classified in the ENZYME databank. In addition, the database is to house much if not all of the information on metabolic pathways currently available from public sources and the literature.
GENEVESTIGATOR
A popular multi-organism gene expression and pathways database and online analysis tool. Users can look at how genes of interest are expressed in many different tissues, developmental stages, stimuli/diseases/drugs, and mutations. These summarized profiles are compiled from thousands of Affymetrix microarrays (as of May 2008: >20,000 arrays from human, mouse, rat, arabidopsis, and barley). Tools for biomarker search, clustering and pathway analysis in these contexts are also available. The tool was developed at the Swiss Federal Institute of Technology in Zurich and is commercialized by NEBION AG.
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CYGD Pathways
MIPS Comprehensive Yeast Genome Database. Search by pathways including amino acid, nucleotide, carbohydates, and lipid metabolism, or function including energy, cell cycle, transcription, protein targetting, intracellular transport and signal transduction.
The aMAZE LightBench
A web interface to a relational database of cellular processes. Web interface to the aMAZE relational database, which contains information on gene expression, catalysed chemical reactions, regulatory interactions, protein assembly, as well as metabolic and signal transduction pathways. It allows the user to browse the information in an intuitive way, which also reflects the underlying data model. Moreover links are provided to literature references, and whenever appropriate, to external databases.
Reactome
Curated database of primarily human biological processes. Curated database of biological processes in humans. Dual-purpose project that can be used by general biologists as an online textbook of biology, or by bioinformaticians to make discoveries about biological pathways. Reactome supersedes an earlier project called The Genome Knowledgebase and incorporates all the information previously available in its predecessor. Reactome sports a radically redesigned user interface in which the entire set of human pathways known to the database is represented as a series of constellations in a starry sky. The starry sky can be used to navigate through the universe of human reactions and is invaluable to visualize connections between pathways, some of which will be surprising to biologists who are not familiar with pathways outside their domain of research. Also new in Reactome are cross-references to the online databases PubMed, UniProt, LocusLink, Ensembl and the Gene Ontology. Product of a partnership between Cold Spring Harbor Lab (CSHL) and EMBL-EBI.
BRENDA (BRaunschweig ENzyme DAtabase) is the largest publicly available enzyme data system worldwide, whose contents are manually extracted from the literature includes data on all identified enzymes. Includes functional, structural, sequence, localisation, disease-related, isolation, stability information on enzyme and ligand-related data, linked to the enzyme source and reference. Complemented by text-mining data in AMENDA (Automatic Mining of ENzyme DAta) and FRENDA (Full Reference ENzyme DAta). Searchable via a genome browser, membrane protein prediction and full-text search and SOAP. The BRENDA data can be downloaded as flat file.
BiologicalNetworks
PathSys is a graph-based system for creating a combined database of biological pathways, gene regulatory networks and protein interaction maps.
BiologicalNetworks: visualization and analysis tool for systems biology
BiologicalNetworks addresses the need for systematic presentation and analysis of high-throughput expression data by mapping and analysis of expression profiles of genes or proteins simultaneously on to regulatory, metabolic and cellular networks.
Roche Biochemical Pathways
ExPASy Home page. Site Map. Search ExPASy. Contact us. ENZYME. Hosted by SIB Switzerland. Mirror sites: Australia. Brazil. Canada. China. Korea. The ExPASy Server requires Javascript to be fully functional. You may not see all the ...
Yeast BioChemical Pathways
Database of
yeast metabolic pathways developed by the SGD project.
Also see Network/pathway reconstruction and analysis Journal Watch
