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A comparative account of pathways, feature-validations and application-based categorizations : Pathways in Arabidopsis
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
Arabidopsis Reactome
http://www.arabidopsisreactome.org
Curated resource of pathways and reactions in plant biology.
Tsesmetzis N, Couchman M, Higgins J, Smith A, Doonan JH, Seifert GJ, Schmidt EE, Vastrik I, Birney E, Wu G, D'Eustachio P, Stein LD, Morris RJ, Bevan MW, Walsh SV. Arabidopsis reactome: a foundation knowledgebase for plant systems biology. Plant Cell. 2008 Jun;20(6):1426-36. Epub 2008 Jun 30. PubMed PMID:18591350; PubMed Central PMCID: PMC2483364.
2008
100
AraCyc
http://www.arabidopsis.org/biocyc
Tool for visualizing the biochemical pathways in Arabidopsis thaliana.
Mueller LA, Zhang P, Rhee SY. AraCyc: a biochemical pathway database for Arabidopsis. Plant Physiol. 2003 Jun;132(2):453-60. PubMed PMID: 12805578; PubMed Central PMCID: PMC166988.
2003
100
Biopath - Database on Biochemical Pathways
http://www.molecular-networks.com/databases/biopath
Contains biological transformation and regulations derived from the Roche Applied Science "biochemical pathways" wall chart.
Schreiber F. High quality visualization of biochemical pathways in BioPath. In Silico Biol. 2002;2(2):59-73. PubMed PMID: 12066841.
2002
100
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
Cyclebase.org
http://www.cyclebase.org
Resource of cell cycle datasets.
Gauthier NP, Larsen ME, Wernersson R, de Lichtenberg U, Jensen LJ, Brunak S, Jensen TS. Cyclebase.org--a comprehensive multi-organism online database of cell-cycle experiments. Nucleic Acids Res. 2008 Jan;36(Database issue):D854-9.Epub 2007 Oct 16. PubMed PMID: 17940094; PubMed Central PMCID: PMC2238932.
2007
100
DRASTIC - Database Resource for Analysis of Signal Transduction In Cells
http://www.drastic.org.uk
A database of plant expressed sequence tags and genes up- and down-regulated in response to pathogen or stress condition.
Button DK, Gartland KM, Ball LD, Natanson L, Gartland JS, Lyon GD. DRASTIC--INSIGHTS: querying information in a plant gene expression database. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D712-6. PubMed PMID: 16381965; PubMed Central PMCID: PMC1347498.
2006
100
URL: temporarily unavailable (10/01/2012).
FMM - From Metabolite to Metabolite
http://FMM.mbc.nctu.edu.tw
Reconstruct the pathway from one metabolite to another, comparison of the pathway among species.
Chou CH, Chang WC, Chiu CM, Huang CC, Huang HD. FMM: a web server for metabolic pathway reconstruction and comparative analysis. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W129-34. Epub 2009 Apr 28. PubMed PMID: 19401437; PubMed Central PMCID: PMC2703958.
2009
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.
GON - Genomic Object Net
http://genome.ib.sci.yamaguchi-u.ac.jp/~gon/index
Software platform for biological pathway modeling and simulation.
Matsuno H, Doi A, Nagasaki M, Miyano S. Hybrid Petri net representation of gene regulatory network. Pac Symp Biocomput. 2000:341-52. PubMed PMID: 10902182.
2000
100
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
MetaCore
http://www.genego.com/metacore.php
Database of molecular cellular pathways, and is designed to integrate data from different levels of cellular function.
Ekins S, Nikolsky Y, Bugrim A, Kirillov E, Nikolskaya T. Pathway mapping tools for analysis of high content data. Methods Mol Biol. 2007;356:319-50. Review. PubMed PMID: 16988414.
2007
100
License required to access the resource.
MetaCrop
http://pgrc-35.ipk-gatersleben.de/pls/htmldb_pgrc/f?p=269:111:802960176267400
Hand-curated information of major metabolic pathways in crops.
Grafahrend-Belau E, Weise S, Koschützki D, Scholz U, Junker BH, Schreiber F. MetaCrop: a detailed database of crop plant metabolism. Nucleic Acids Res. 2008 Jan;36(Database issue):D954-8. Epub 2007 Oct 11. PubMed PMID: 17933764; PubMed Central PMCID: PMC2238923.
2007
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
MetNetDB - MetNet (Metabolic Network Exchange) database
http://www.metnetdb.org/MetNet_db.htm
Information on metabolic and regulatory interactions in Arabidopsis.
Wurtele ES, Li J, Diao L, Zhang H, Foster CM, Fatland B, Dickerson J, Brown A, Cox Z, Cook D, Lee EK, Hofmann H. MetNet: Software to Build and Model the Biogenetic Lattice of Arabidopsis. Comp Funct Genomics. 2003;4(2):239-45. PubMed PMID: 18629120; PubMed Central PMCID: PMC2447407.
2003
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
PathoPlant
http://www.pathoplant.de
Plant pathogenesis pathways and interactions.
Bülow L, Schindler M, Choi C, Hehl R. PathoPlant: a database on plant-pathogen interactions. In Silico Biol. 2004;4(4):529-36. PubMed PMID: 15752070.
2004
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
PhosPhAt - Arabidopsis Protein Phosphorylation Site Database
http://phosphat.mpimp-golm.mpg.de
Resource of mass spectrometry based phosphorylation sites in Arabidopsis.
Heazlewood JL, Durek P, Hummel J, Selbig J, Weckwerth W, Walther D, Schulze WX. PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor. Nucleic Acids Res. 2008 Jan;36(Database issue):D1015-21. Epub 2007 Nov 4. PubMed PMID: 17984086; PubMed Central PMCID: PMC2238998.
2007
100
Protein Lounge
http://www.proteinlounge.com
Contains curated pathways for many different organisms.
Not available
Not available
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
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
 
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