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Links tagged with 'metabolism'

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BioCyc Knowledge LibraryDatabase Content

http://www.biocyc.org/

Protein > Interactions, Pathways, Enzymes

BioCyc is a collection of pathway/genome databases derived either from the literature (EcoCyc and MetaCyc) or computationally (ie. HumanCyc). EcoCyc is used to visualize gene layout, biochemical reactions, and pathways for the E. coli chromosome; MetaCyc contains the enzymes, reactions, and pathways for a variety of organisms (mostly micro-organisms)

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tagsbacterial gene expression regulation bacterial genome database management systems enzymes escherichia coli escherichia coli proteins genetic databases genome humans metabolism protein databases protein transport signal transduction

GenePublisherTool Content

http://www.cbs.dtu.dk/services/GenePublisher

Expression > Transcript Expression Analysis

GenePublisher performs automatic normalization, statistical analysis, and visualization of DNA microarray data.

NAR Web Server Issue 2003
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tagsautomation cluster analysis gene expression profiling genetic databases genetic promoter regions metabolism nucleic acid regulatory sequences oligonucleotide array sequence analysis signal transduction

HMDBDatabase Content

http://www.hmdb.ca/

Human Genome > Other Resources
Other Molecules > Metabolites

The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. The database supports extensive text, sequence, chemical structure and relational query searches.

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tagsbiochemical phenomena biochemistry biomolecular nuclear magnetic resonance humans metabolism organ transplantation

KEGG: Kyoto Encyclopedia of Genes and GenomesDatabase Content

http://www.genome.ad.jp/kegg/

Expression > Networks
Protein > Interactions, Pathways, Enzymes
Protein > Proteomics

Pathway maps, molecular catalogs, genome maps and gene catalogs that capture knowledge about interactions in terms of information pathways. KEGG comprises several databases, including BRITE (protein-protein interactions), PATHWAY (interaction networks for cellular processes), and LIGAND (chemical compounds and chemical reactions). KEGG Atlas is a new tool for the global analysis of metabolic pathways.

NAR Web Server Issue 2008
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tagsamino acid sequence animals biological models computational biology computer simulation disease factual databases gene expression genes genetic models genome genomics humans japan ligands metabolic networks and pathways metabolism molecular sequence data molecular structure pharmaceutical preparations protein binding proteome sequence homology systems biology systems integration

MetaPath OnlineTool Content

http://scopes.biologie.hu-berlin.de/

Other Molecules > Metabolites
Protein > Interactions, Pathways, Enzymes

MetaPath Online gives users access to an algorithm for network expansion. Starting with given metabolites, called seed compounds, the algorithm uses known information about metabolic reactions and pathways to expand the network and define scope. This systematic investigation of structure-function relationships of metabolic networks can offer evolutionary insights.

NAR Web Server Issue 2007
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tagsadenosine triphosphate algorithms animals archaea bacteria biological evolution biological models cell physiological phenomena chemical models coenzymes computational biology computer simulation energy metabolism eukaryotic cells factual databases gene expression profiling genetic models genetic variation glucose glycolysis humans inorganic chemicals kinetics metabolism molecular evolution nerve net organic chemicals phosphates phylogeny physiological adaptation protein biosynthesis proteins signal transduction species specificity substrate specificity

metaSHARKTool Content

http://bioinformatics.leeds.ac.uk/shark/

Protein > Interactions, Pathways, Enzymes

Metabolic Search And Reconstruction Kit (metaSHARK) provides an interactive visualisation platform for the KEGG metabolic network in the form of the SHARKview applet.

NAR Web Server Issue 2006
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tagsanimals biological models coenzyme a dna sequence analysis eimeria tenella enzymes gene expression profiling genomics metabolism plasmodium falciparum protozoan genome

PathExpressTool Content

http://bioinfoserver.rsbs.anu.edu.au/utils/PathExpress/

Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

PathExpress is a tool developed to interpret gene expression data obtained from microarray experiments by identifying and visualizing the most relevant metabolic pathways associated with a subset of genes (e.g. differentially expressed genes). Enzyme Neighborhood (a sub-network of linked enzymes with a limited path length) allows identification of the most relevant sub-network affected in a gene expression experiment.

This content is being maintained by ngoffard.

NAR Web Server Issue 2007NAR Web Server Issue 2009
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tagsalgorithms animals biological models computational biology database management systems enzymes gene expression profiling humans medicago truncatula metabolic networks and pathways metabolism oligonucleotide array sequence analysis protein interaction mapping

PathGuideResource Content

http://www.pathguide.org/

Education > Directories and Portals
Protein > Interactions, Pathways, Enzymes

The PathGuide - Pathway Resource List (PRL) is a database of 250+ links to resources for protein-protein interactions, metabolic and signalling pathways, transcription factor and genetic interaction networks, pathway diagrams, protein sequences, and protein-compound interactions.

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tagsgene expression regulation genetic databases metabolism proteins signal transduction systems integration transcription factors

Pathway extractionTool Content

http://rsat.bigre.ulb.ac.be/rsat/index_neat.html

Protein > Interactions, Pathways, Enzymes

The pathway extraction tool is a part of the network analysis tool suite (NeAT). Given a metabolic network, the tool extracts a subnetwork that connects a list of input compounds, reactions, EC numbers or enzyme-coding genes. Three metabolic networks (KEGG LIGAND, KEGG RPAIR and MetaCyc) are preloaded, but custom networks can be submitted as well.

This content is being maintained by karoline.

NAR Web Server Issue 2005
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tagsmetabolic networks metabolic pathway metabolism path finding pathfinding subnetwork subnetworks

PolySearchTool Content

http://wishart.biology.ualberta.ca/polysearch

Literature > Text Mining and Semantics

PolySearch allows users to conduct comprehensive and associative queries, such as given X, find all Y's, where X or Y can be diseases, tissues, cell compartments, gene/protein names, SNPs, mutations, drugs and metabolites. PolySearch also identifies, highlights and ranks abstracts, paragraphs or sentences.

NAR Web Server Issue 2008
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tagsalgorithms factual databases genes humans inborn genetic diseases metabolism mutation pharmaceutical preparations pubmed

SEARCHGTrTool Content

http://www.nii.res.in/searchgtr.html

Other Molecules > Carbohydrates
Protein > Domains and Motifs

SEARCHGTr is a tool for the analysis of glycosyltransferases (GTrs) that allows you to compare a query sequence with the sequences of characterized GTrs.

NAR Web Server Issue 2005
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tagsanti-bacterial agents binding sites computational biology glycosylation glycosyltransferases metabolism protein conformation protein sequence analysis substrate specificity

Systems Biology Markup Language (SBML)Resource Content

http://www.sbml.org/

Computer Related > Bio-* Programming Tools

The Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biochemical reaction networks. SBML is applicable to metabolic networks, cell-signaling pathways, genomic regulatory networks, and many other areas in systems biology.

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tagsbiological models chemical models controlled vocabulary database management systems documentation factual databases gene expression regulation metabolism programming languages software design terminology as topic

VisANTTool Content

http://visant.bu.edu/

Expression > Gene Set Analysis
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, as a java web application, or downloaded and run locally. New functions in VisANT 3.5 allow determination of over-representation and expression enrichment.

NAR Web Server Issue 2005NAR Web Server Issue 2007NAR Web Server Issue 2009
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tagsalgorithms animals biological models caenorhabditis elegans cell cycle computational biology computer simulation database management systems drosophila fungal genes gene expression profiling gene expression regulation gene regulatory networks genetic databases genetic models genetic transcription genome helminth genes helminth proteins humans macromolecular substances metabolism mice protein databases protein interaction mapping proteome saccharomyces cerevisiae saccharomyces cerevisiae proteins signal transduction software design systems integration three-dimensional imaging transcription factors two-hybrid system techniques