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UCSD-Nature Signaling Gateway Molecule Pages

http://www.signaling-gateway.org/molecule/

Description :
Expert-authored and peer-reviewed information on mammalian proteins involved in cellular signaling

BRITE - Biomolecular Relations in Information Transmission and Expression

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

Description :
Molecular interactions and pathways database, part of the KEGG system

HMDB

http://www.hmdb.ca/

Description :
Human Metabolome Database

MedicCyc

http://www.noble.org/mediccyc/

Description :
Biochemical pathways in Medicago truncatula

MetaCrop

http://metacrop.ipk-gatersleben.de/

Description :
Biochemical pathways and enzymes in crop plants

MiST - Microbial Signal Transduction database

http://genomics.ornl.gov/mist

Description :
Signal transduction systems link environmental stimuli with adaptive cellular responses and enable an organism to survive and adapt to changing conditions. This communication network of signaling pathways regulates critical cellular activities in all organisms from bacteria to humans. The MiST (Microbial Signal Transduction) database is a comprehensive catalog of the signal transduction proteins (two- and one-component systems) within completely sequenced bacterial and archaeal genomes. These are identified with various domain profiles that directly or indirectly implicate a particular protein as participating in signal transduction. MiST currently contains information on the signal transduction proteins within more than 365 genomes and newly, available genomes are added on a monthly basis. We have designed a user-friendly interface to facilitate the comparison and analysis of bacterial signal transduction repertoires.

Aknowledgement :
We thank the BLAST/STIM research community for many valuable discussions and suggestions on the MiST scope and development. We are grateful to Jan Lukens and "Friends of the Zhulin lab" for their contribution toward our Linux cluster. This work was supported in part by a grant GM072285 from the National Institutes of Health to I.B.Z. and funds provided by the UT-ORNL Joint Institute for Computational Sciences.

References :
Ulrich, LE and Zhulin, IB. (2007) MiST - Microbial Signal Transduction Database. Nucleic Acids Research. 35: in press.

NetworKIN

http://networkin.info/

Description :
Network approach to human protein kinases and their substrate proteins

PathoPlant®

http://www.pathoplant.de/

Description :
PathoPlant® has been developed as a relational database to display relevant components and reactions involved in signal transduction related to plant-pathogen interactions. Signal transduction pathways are modeled as consecutive sequences of known molecules and corresponding reactions. PathoPlant entries are linked to associated internal records as well as to entries in external databases such as SWISS-PROT, GenBank, TAIR, AthaMap, PubMed, and TRANSFAC®. PathoPlant has recently been complemented by microarray gene expression data from Arabidopsis thaliana subjected to pathogen infection and elicitor treatment. Implemented web tools enable identification of plant genes regulated by specific stimuli. Up to three stimuli can be combined with the option of induction factor restriction to determine similarly regulated genes. To identify common cis-regulatory elements in co-regulated genes, a resulting gene list can directly be exported to the AthaMap database (http://www.athamap.de) for analysis.

Aknowledgement :
We would like to thank Thomas Zobel, Daniela Bruhn and Juliane Scheithauer for data annotation. The PathoPlant® project is supported by the German Federal Ministry for Education and Research, BMBF, Grant No. 031U110C/031U210C.

References :
1. Bülow, L., Schindler, M., Choi, C. and Hehl R. (2004) PathoPlant®: a database on plant-pathogen interactions. In Silico Biol., 4, 0044.

STCDB - Signal Transduction Classification Database

http://bibiserv.techfak.uni-bielefeld.de/stcdb/

Description :
Signal Transduction Classification Database (STCDB, http://www.techfak.uni-bielefeld.de/~mchen/STCDB/) contains general information on signal transduction classification. It includes links to individual documents, the number of which will increase as more sections of the signal transduction list are revised. It also provides advice on how to suggest new signal transductions for listing or correction of existing entries.

Recent develoments :
A new web-based search engine and a graphical tool for viewing the network of interactive signal transductions will soon be available.

Aknowledgement :
This work is supported in part by the German Research Foundation (DFG) and the German Academic Exchange Service (DAAD).

VirHostNet

http://pbildb1.univ-lyon1.fr/virhostnet

Description :
A knowledgebase of virus-host molecular interaction networks

PID

http://pid.nci.nih.gov/

Description :
NCI-Nature Pathway Interaction Database

Pathway Resource List

http://www.cbio.mskcc.org/prl/index.php

Description :
The Pathway Resource List (PRL) is a database of 150+ 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.

ProdoNet

http://www.prodonet.tu-bs.de/

Description :
A web-based application for the mapping of prokaryotic genes and the corresponding proteins to common gene regulatory and metabolic networks. Users input a list of genes from which shared operons, co-expressed genes and shared regulators are detected. Common metabolic pathways are then viewed on KEGG maps.

PaLS

http://pals.bioinfo.cnio.es/

Description :
Pathway and Literature Strainer (PaLS) highlights those members on a user inputted list that share descriptors from PubMed, GO, KEGG and Reactome.

CPA - Comparative Pathway Analyzer

https://www.cebitec.uni-bielefeld.de/groups/brf/software/cpa/index.html

Description :
The Comparative Pathway Analyzer (CPA) is a web tool for comparative metabolic network analysis. The differences in metabolic reaction content between two sets of organisms are computed and displayed on KEGG pathway maps.

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