Home   |  About Startbioinfo | Other web-portals 

Categories of resources

Suggested Readings
 
 
Total resources - 18
A comparative account of pathways, feature-validations and application-based categorizations : Pathways in C. elegans
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
CPA - Comparative Pathway Analyzer
http://cpa.cebitec.uni-bielefeld.de
Investigates reaction content of a set of organisms.
Oehm S, Gilbert D, Tauch A, Stoye J, Goesmann A. Comparative Pathway Analyzer--a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W433-7. Epub 2008 Jun 6. PubMed PMID: 18539612; PubMed Central PMCID: PMC2447754.
2008
100
GeneMANIA
http://www.genemania.org
Finds other genes related to a set of input genes, using a very large set of functional association data.
Mostafavi S, Ray D, Warde-Farley D, Grouios C, Morris Q. GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function. Genome Biol. 2008;9 Suppl 1:S4. Epub 2008 Jun 27. PubMed PMID: 18613948; PubMed Central PMCID: PMC2447538.
2008
100
Requires JAVA +5.0.
Genepath
http://www.genepath.org/genepath2
Web based application for the analysis of mutation based experiments.
Demsar J, Zupan B, Bratko I, Kuspa A, Halter JA, Beck RJ, Shaulsky G. GenePath: a computer program for genetic pathway discovery from mutant data. StudHealth Technol Inform. 2001;84(Pt 2):956-9. PubMed PMID: 11604873.
2001
100
URL could not be retrieved (10/01/2012).
JWS - Java Web Simulation
http://jjj.biochem.sun.ac.za
Repository of kinetic models describing biological systems which can be interactively run and interrogated over the internet.
Snoep JL, Olivier BG. Java Web Simulation (JWS); a web based database of kinetic models. Mol Biol Rep. 2002;29(1-2):259-63. PubMed PMID: 12241068.
2002
100
KEGG - Kyoto Encyclopedia of Genes and Genomes
http://www.genome.jp/kegg
Database of metabolic pathways from different organisms, also provides reference pathways that describe a general pathway which is then projected onto a genome based on the presence of pathway enzymes in that genome.
Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 1999 Jan 1;27(1):29-34.PubMed PMID: 9847135; PubMed Central PMCID: PMC148090.
1999
100
METAPATH
http://scopes.biologie.hu-berlin.de/index.php?m=path
Calculation of minimal synthesis pathway.
Handorf T, Ebenhöh O. MetaPath Online: a web server implementation of the network expansion algorithm. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W613-8. Epub 2007 May 5. PubMed PMID: 17483511; PubMed Central PMCID:PMC1933239.
2007
100
MetExplore
http://metexplore.toulouse.inra.fr/metexploreJoomla/index.php
A web resource that offers the possibility to link the metabolites identified in untargetted metabolomics experiments within the context of genome scale reconstructed metabolic network.
Cottret L, Wildridge D, Vinson F, Barrett MP, Charles H, Sagot MF, Jourdan F. MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W132-7. Epub 2010 May 5. PubMed PMID: 20444866; PubMed Central PMCID: PMC2896158.
2010
100
MiMI - Michigan Molecular Interactions
http://mimi.ncibi.org/MimiWeb/main-page.jsp
Contains pathway diagrams from KEGG and Reactome.
Jayapandian M, Chapman A, Tarcea VG, Yu C, Elkiss A, Ianni A, Liu B, Nandi A, Santos C, Andrews P, Athey B, States D, Jagadish HV. Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. Nucleic Acids Res. 2007 Jan;35(Database issue):D566-71. Epub 2006 Nov 27. PubMed PMID: 17130145; PubMed Central PMCID: PMC1716720.
2006
100
NCBI BioSystems
http://www.ncbi.nlm.nih.gov/biosystems
Connects biosystem records with the associated literature, molecular and chemical data.
Evsikov AV, Dolan ME, Genrich MP, Patek E, Bult CJ. MouseCyc: a curated biochemical pathways database for the laboratory mouse. Genome Biol. 2009;10(8):R84. Epub 2009 Aug 14. PubMed PMID: 19682380; PubMed Central PMCID:PMC2745765.
2009
100
PANTHER - Protein ANalysis Through Evolutionary Relationships
http://www.pantherdb.org
Gene expression data analysis, comparison of gene lists.
Mi H, Lazareva-Ulitsky B, Loo R, Kejariwal A, Vandergriff J, Rabkin S, Guo N, Muruganujan A, Doremieux O, Campbell MJ, Kitano H, Thomas PD. The PANTHERdatabase of protein families, subfamilies, functions and pathways. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D284-8. PubMed PMID: 15608197; PubMed Central PMCID: PMC540032.
2005
100
Pathway Commons
http://www.pathwaycommons.org/pc/
Provides researchers with convenient access to the collection of publicly available pathways from many different organisms.
Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, Schultz N, Bader GD, Sander C. Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res. 2011 Jan;39(Database issue):D685-90. Epub 2010 Nov 10. PubMed PMID: 21071392; PubMed Central PMCID: PMC3013659.
2010
100
Protein Lounge
http://www.proteinlounge.com
Contains curated pathways for many different organisms.
Not available
Not available
100
pSTIING - Protein, Signalling, Transcriptional Interactions & Inflammation Networks Gateway
http://pstiing.licr.org
Intergrated database of molecular association and transcriptional regulatory networks.
Ng A, Bursteinas B, Gao Q, Mollison E, Zvelebil M. pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D527-34. PubMed PMID: 16381926; PubMed Central PMCID: PMC1347407.
2006
100
R spider
http://mips.helmholtz-muenchen.de/proj/rspider
Analysis of the list of genes, exploiting the KEGG and Reactome Knowledgebases.
Antonov AV, Schmidt EE, Dietmann S, Krestyaninova M, Hermjakob H. R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W78-83. Epub 2010 Jun 2. PubMed PMID: 20519200; PubMed Central PMCID: PMC2896180.
2010
100
SignaLink
http://signalink.org
Allows system level analysis using the network of intracellular signaling pathways.
Korcsmáros T, Farkas IJ, Szalay MS, Rovó P, Fazekas D, Spiró Z, Böde C, Lenti K, Vellai T, Csermely P. Uniformly curated signaling pathways reveal tissue-specific cross-talks and support drug target discovery. Bioinformatics. 2010 Aug 15;26(16):2042-50. Epub 2010 Jun 11. PubMed PMID: 20542890.
2010
100
TRRD - Transcription Regulatory Regions Database
http://wwwmgs.bionet.nsc.ru/mgs/gnw/trrd
Information on the structural and functional organization of transcription regulatory regions in the eukaryotic genes.
Kel' AE, Kolchanov NA, Kel' OV, Romashchenko AG, Anan'ko EA, Ignat'eva EV, Merkulova TI, Podkolodnaia OA, Stepanenko IL, Kochetov AV, Kolpakov FA,Podkolodnyi NL, Naumochkin AA. [TRRD: a database of transcription regulatory regions in eukaryotic genes]. Mol Biol (Mosk). 1997 Jul-Aug;31(4):626-36.Russian. PubMed PMID: 9340490.
1997
100
VisANT
http://visant.bu.edu
Visual analysis tool for biological networks, predict the function of a network module.
Hu Z, Mellor J, Wu J, DeLisi C. VisANT: an online visualization and analysis tool for biological interaction data. BMC Bioinformatics. 2004 Feb 19;5:17. PubMed PMID: 15028117; PubMed Central PMCID: PMC368431.
2004
100
WikiPathways
http://wikipathways.org
Open, public space for pathway editing.
Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C.WikiPathways: pathway editing for the people. PLoS Biol. 2008 Jul 22;6(7):e184.PubMed PMID: 18651794; PubMed Central PMCID: PMC2475545.
2008
100
 
Disclaimer
Grow and let grow!
copyright © shodhaka life sciences private limited; all rights reserved

Internet Coupons
xanga traffic