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A comparative account of pathways, feature-validations and application-based categorizations : Pathways in yeast
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
BioCyc
http://biocyc.org
Gene interactions in dynamic graphical models, depicts molecular relationships.
Krummenacker M, Paley S, Mueller L, Yan T, Karp PD. Querying and computing with BioCyc databases. Bioinformatics. 2005 Aug 15;21(16):3454-5. Epub 2005 Jun16. PubMed PMID: 15961440; PubMed Central PMCID: PMC1450015.
2005
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
BRENDA - BRaunschweig ENzyme Database
http://www.brenda-enzymes.info
Protein function database that gives details of the metabolic reactions.
Schomburg I, Chang A, Schomburg D. BRENDA, enzyme data and metabolic information. Nucleic Acids Res. 2002 Jan 1;30(1):47-9. PubMed PMID: 11752250; PubMed Central PMCID: PMC99121.
2002
100
CellCircuits
http://www.cellcircuits.org
Open-circuit database of network model.
Mak HC, Daly M, Gruebel B, Ideker T. CellCircuits: a database of protein network models. Nucleic Acids Res. 2007 Jan;35(Database issue):D538-45. Epub 2006 Nov 29. PubMed PMID: 17135207; PubMed Central PMCID: PMC1751555.
2007
100
License required to access the resource.
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
DRYGIN
http://drygin.ccbr.utoronto.ca
Database of quantitative genetic interactions in yeast.
Koh JL, Ding H, Costanzo M, Baryshnikova A, Toufighi K, Bader GD, Myers CL, Andrews BJ, Boone C. DRYGIN: a database of quantitative genetic interaction networks in yeast. Nucleic Acids Res. 2010 Jan;38(Database issue):D502-7. Epub2009 Oct 30. PubMed PMID: 19880385; PubMed Central PMCID: PMC2808960.
2010
100
EMP - Enzymes and Metabolic Pathways Database
http://www.empproject.com
Electronic source of biochemical data that stores details like chemical reactions and Km.
Selkov E, Basmanova S, Gaasterland T, Goryanin I, Gretchkin Y, Maltsev N, Nenashev V, Overbeek R, Panyushkina E, Pronevitch L, Selkov E Jr, Yunus I. The metabolic pathway collection from EMP: the enzymes and metabolic pathways database. Nucleic Acids Res. 1996 Jan 1;24(1):26-8. PubMed PMID: 8594593; PubMed Central PMCID: PMC145618.
1996
100
URL could not be retrieved (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.
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
MassTRIX
http://metabolomics.helmholtz-muenchen.de/masstrix2
Annotates metabolites in high precision mass spectrometry data.
Suhre K, Schmitt-Kopplin P. MassTRIX: mass translator into pathways. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W481-4. Epub 2008 Apr 28. PubMed PMID:18442993; PubMed Central PMCID: PMC2447776.
2007
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.
MetaCyc - Metabolic Pathway Database
http://metacyc.org
Contains pathways from different organisms.
Krieger CJ, Zhang P, Mueller LA, Wang A, Paley S, Arnaud M, Pick J, Rhee SY, Karp PD. MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D438-42. PubMed PMID: 14681452; PubMed Central PMCID: PMC308834.
2004
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
MIPS CYGD - MIPS Comprehensive Yeast Genome Database
http://mips.helmholtz-muenchen.de/genre/proj/yeast
Gathers and merges data from protein interaction databases making it convenient to visualize the combined set.
Mewes HW, Amid C, Arnold R, Frishman D, Güldener U, Mannhaupt G, Münsterkötter M, Pagel P, Strack N, Stümpflen V, Warfsmann J, Ruepp A. MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D41-4. PubMed PMID: 14681354; PubMed Central PMCID:PMC308826.
2004
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
PathFinder
http://pathfinder.nimh.nih.gov
Mining signal transduction pathway segments from protein-protein interaction networks.
Bebek G, Yang J. PathFinder: mining signal transduction pathway segments from protein-protein interaction networks. BMC Bioinformatics. 2007 Sep 13;8:335.PubMed PMID: 17854489; PubMed Central PMCID: PMC2100073.
2007
100
URL could not be retrieved (10/01/2012).
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
PHT - Pathway Hunter Tool
http://pht.tu-bs.de
Finds all the shortest valid pathways that connect two molecules, statistical information about different pathways in different organisms.
Rahman SA, Advani P, Schunk R, Schrader R, Schomburg D. Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC). Bioinformatics. 2005 Apr1;21(7):1189-93. Epub 2004 Nov 30. PubMed PMID: 15572476.
2005
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
ResponseNet
http://bioinfo.bgu.ac.il/respnet
Reveals signaling and regulatory networks linking genetic and transcriptomic screening data.
Lan A, Smoly IY, Rapaport G, Lindquist S, Fraenkel E, Yeger-Lotem E.ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W424-9. Epub 2011 May 16. PubMed PMID: 21576238; PubMed Central PMCID:PMC3125767.
2011
100
The SEED
http://theseed.uchicago.edu/FIG/index.cgi
Annotation and analysis tool for microbial genomes.
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A,Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I,Vassieva O, Ye Y, Zagnitko O, Vonstein V. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 2005 Oct 7;33(17):5691-702. Print 2005. PubMed PMID: 16214803; PubMed Central PMCID: PMC1251668.
2005
100
TORQUE - Topology-Free Querying of Protein Interaction Networks
http://www.cs.tau.ac.il/~bnet/torque.html
Information regarding protein interaction networks.
Bruckner S, Hüffner F, Karp RM, Shamir R, Sharan R. Topology-free querying of protein interaction networks. J Comput Biol. 2010 Mar;17(3):237-52. PubMed PMID: 20377443.
2010
100
Installation required.
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
YeastCyc - Yeast Biochemical Pathway Database
http://pathway.yeastgenome.org
Manually curated collection of S. cerevisiae pathways, primarily curated from scientific literature.
Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D311-4. PubMed PMID: 14681421; PubMed Central PMCID: PMC308767.
2004
100
YEASTNET - A consensus reconstruction of yeast metabolism
http://www.comp-sys-bio.org/yeastnet
Consensus network model for yeast metabolomics.
Herrgard MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Bluthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novere N, Li P, Liebermeister W,Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasic I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttila M, Klipp E, Palsson BØ, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol. 2008 Oct;26(10):1155-60. PubMed PMID: 18846089.
2008
100
 
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