Links tagged with 'signal transduction'

Found 39 links

Displaying 15 links

BioCyc Knowledge LibraryDatabase Content

http://www.biocyc.org/

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)

BiologicalNetworksTool Content

http://brak.sdsc.edu/pub/BiologicalNetworks/

BiologicalNetworks allows retrieval, construction, and visualization of biological networks and allows for the analysis of high-throughput expression data by mapping onto network graphs. BiologicalNetworks queries the PathSys system, a combined database of biological pathways, gene regulatory networks, and protein interaction maps.

BioPaxResource Content

http://www.biopax.org/

The BioPAX web site provides information about a collaborative effort to create a data exchange format for biological pathways.

ConsensusPathDBDatabase Content

http://cpdb.molgen.mpg.de

ConsensusPathDB is a meta-database that integrates physical protein interactions, metabolic and signaling reactions and gene regulatory interactions in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. ConsensusPathDB offers different ways of utilizing these integrated interaction data, with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways.

DEEPTool Content

http://www.bioinf.med.uni-goettingen.de/services/deep/

DEEP (Differential Expression Effector Prediction) is a tool that can identify effectors of specific expression profiles by combining gene expression data with biological expert knowledge about biomolecular interaction networks (provided by resources like TRANSPATH, for example).

EcoCycDatabase Content

http://EcoCyc.org

EcoCyc is a comprehensive model organism database for Escherichia coli K-12 MG1655. From the scientific literature, EcoCyc captures the functions of individual E. coli gene products; their regulation at the transcriptional, post-transcriptional and protein level; and their organization into operons, complexes and pathways. EcoCyc users can search and browse the information in multiple ways. New features include combined gene/protein pages and a Regulation Summary Diagram displaying a graphical overview of all known regulatory inputs to gene expression and protein activity.

iHOPTool Content

http://www.ihop-net.org/UniPub/iHOP/

iHOP (Information Hyperlinked over Proteins) allows researchers to explore a network of gene and protein interactions based on published scientific literature. For each gene search, iHOP reports sentences from abstracts associating it with other genes, links out to full abstracts, and reports experimental evidence for the interactions, if available. You can also select sentences to create and visualize your own gene model.

KAASTool Content

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

KAAS (KEGG Automatic Annotation Server) is a tool for ortholog assignment and pathway mapping. KAAS provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database. The result contains KO (KEGG Orthology) assignments and automatically generated KEGG pathways.

KOBASTool Content

http://kobas.cbi.pku.edu.cn

KEGG Orthology-Based Annotation System (KOBAS) annotates sequences with KEGG Orthology terms and identifies the frequently occurring (or significantly enriched) pathways among the queried sequences compared against a background distribution. 5 pathway databases are used (KEGG Pathway, PID, BioCyc, Reactome, Panther) and 5 human databases (OMIM, KEGG Disease, FunDO, GAD, NHGRI GWAS).

LitInspectorTool Content

http://www.litinspector.org/

A literature search tool providing gene homonym mining within the PubMed database. Search terms are highlighted in the results. LitInspector also performs signal transduction pathway mining using a manually curated database of pathway names, pathway components and pathway keywords.