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Total resources - 192
Pathways

S.NoResources

Important features / utilities*CitationsYear of publicationRank by usage frequency Add comments
1 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.
Toyoda T, Konagaya A. KnowledgeEditor: a new tool for interactive modeling and analyzing biological pathways based on microarray data. Bioinformatics. 2003 Feb12;19(3):433-4. PubMed PMID: 12584137.
1999
34
2 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 CrE9cy-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, RFCckert 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
65
3 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.
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.
2002
67
4 ExPASy Biochemical Pathway Maps
http://web.expasy.org/pathways		 Entering a keyword search can provide an image of that area on the wall chart with an ability to navigate around the entire wall chart.
Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A. ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 2003 Jul 1;31(13):3784-8. PubMed PMID: 12824418; PubMed Central PMCID: PMC168970.
2003
73
5 MetaboAnalyst
http://www.metaboanalyst.ca		 A web based metabolic data processing tool.
Grafahrend-Belau E, Weise S, KoschFCtzki 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.
2009
74
6 Reactome
http://www.reactome.org		 Provides process level annotation of the structure and function of the human genome with dynamic link to other databases for human systems.
Stein LD. (2004) Using the Reactome database. Curr Protoc Bioinformatics. Chapter 8:Unit 8.7.
2004
77
7 NeAT - Network Analysis Tools
http://rsat.ulb.ac.be/neat		 Provides a series of modular computer programs designed for analysis of biological network.
Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A. Human Protein Reference Database--2009 update. Nucleic Acids Res. 2009 Jan;37(Database issue):D767-72.Epub 2008 Nov 6. PubMed PMID: 18988627; PubMed Central PMCID: PMC2686490.
2008
79
8 HMDB - Human Metabolome Database
https://hmdb.ca/		 Sequence of enzymes involved in human metabolic pathways.
Wishart DS, Tzur D, Knox C, Eisner R, Guo AC, Young N, Cheng D, Jewell K, Arndt D, Sawhney S, Fung C, Nikolai L, Lewis M, Coutouly MA, Forsythe I, Tang P, Shrivastava S, Jeroncic K, Stothard P, Amegbey G, Block D, Hau DD, Wagner J, Miniaci J, Clements M, Gebremedhin M, Guo N, Zhang Y, Duggan GE, Macinnis GD, Weljie AM, Dowlatabadi R, Bamforth F, Clive D, Greiner R, Li L, Marrie T, Sykes BD, Vogel HJ, Querengesser L. HMDB: the Human Metabolome Database. Nucleic Acids Res. 2007 Jan;35(Database issue):D521-6. PubMed PMID: 17202168; PubMed Central PMCID: PMC1899095.
2007
81
9 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
82
Requires JAVA +5.0.
10 MassTRIX
http://metabolomics.helmholtz-muenchen.de/masstrix2		 Annotates metabolites in high precision mass spectrometry data.
Xia J, Psychogios N, Young N, Wishart DS. MetaboAnalyst: a web server for metabolomic data analysis and interpretation. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W652-60. Epub 2009 May 8. PubMed PMID: 19429898; PubMed CentralPMCID: PMC2703878.
2007
88
11 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
88
12 PID - NCI-Nature Pathway Interaction Database
http://pid.nci.nih.gov		 Provides tools to aid pathway focused analysis of large datasets.
Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, Hannay T, Buetow KH. PID: the Pathway Interaction Database. Nucleic Acids Res. 2009 Jan;37(Database issue):D674-9. Epub 2008 Oct 2. PubMed PMID: 18832364; PubMed Central PMCID:PMC2686461.
2008
88
13 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
91
14 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
92
15 LIPID MAPS - LIPID Metabolites And Pathways Strategy
http://www.lipidmaps.org		 Comprehensive website for lipid biology with maps associated with the lipidomics.
Ginsburg H. Progress in in silico functional genomics: the malaria Metabolic Pathways database. Trends Parasitol. 2006 Jun;22(6):238-40. Epub 2006 May 16.PubMed PMID: 16707276.
2007
93
16 CPDB - ConsensusPathDB
http://cpdb.molgen.mpg.de		 Integrates pathway and functional interaction resources.
Kamburov A, Wierling C, Lehrach H, Herwig R. ConsensusPathDB--a database for integrating human functional interaction networks. Nucleic Acids Res. 2009 Jan;37(Database issue):D623-8. Epub 2008 Oct 21. PubMed PMID: 18940869; PubMed Central PMCID: PMC2686562.
2008
94
17 GenMAPP - Gene MicroArray Pathway Profiler
http://www.genmapp.org		 Computer application, that allows gene expression data on pathway diagrams for various model organisms.
Dahlquist KD, Salomonis N, Vranizan K, Lawlor SC, Conklin BR. GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat Genet.2002 May;31(1):19-20. PubMed PMID: 11984561.
2002
95
Registration required to access the resource.
18 Indigo
http://chlora.lgi.infobiogen.fr:1234/Indigo		 Contains information on codon usage, operons, gene neighbours in case of E. coli and Bacillus subtilis.
Lynn DJ, Winsor GL, Chan C, Richard N, Laird MR, Barsky A, Gardy JL, Roche FM, Chan TH, Shah N, Lo R, Naseer M, Que J, Yau M, Acab M, Tulpan D, Whiteside MD, Chikatamarla A, Mah B, Munzner T, Hokamp K, Hancock RE, Brinkman FS. InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Mol Syst Biol. 2008;4:218. Epub 2008 Sep 2. PubMed PMID: 18766178; PubMed Central PMCID: PMC2564732.
1998
95
19 NCBI BioSystems
http://www.ncbi.nlm.nih.gov/biosystems		 Connects biosystem records with the associated literature, molecular and chemical data.
Geer, L.Y., Marchler-Bauer, A., Geer, R.C., Han, L., He, J., He, S., Liu, C., Shi, W. and Bryant, S.H., 2010. The NCBI biosystems database. Nucleic acids research, 38(suppl_1), pp.D492-D496.
2010
95
20 NetPath
http://www.netpath.org		 A curated resource of signal transduction pathways.
Linding R, Jensen LJ, Ostheimer GJ, van Vugt MA, JF8rgensen C, Miron IM, Diella F, Colwill K, Taylor L, Elder K, Metalnikov P, Nguyen V, Pasculescu A, Jin J,Park JG, Samson LD, Woodgett JR, Russell RB, Bork P, Yaffe MB, Pawson T. Systematic discovery of in vivo phosphorylation networks. Cell. 2007 Jun 29;129(7):1415-26. Epub 2007 Jun 14. PubMed PMID: 17570479; PubMed Central PMCID:PMC2692296.
2009
95
21 NMPDR - National Microbial Pathogen Data Resource
http://www.nmpdr.org		 Microbial pathogen data resource with emphasis on food-borne pathogens.
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.
2007
95
22 PharmGKB
http://www.pharmgkb.org		 Drug action pathways.
Hewett M, Oliver DE, Rubin DL, Easton KL, Stuart JM, Altman RB, Klein TE. PharmGKB: the Pharmacogenetics Knowledge Base. Nucleic Acids Res. 2002 Jan 1;30(1):163-5. PubMed PMID: 11752281; PubMed Central PMCID: PMC99138.
2002
95
23 BioModels database
http://www.ebi.ac.uk/biomodels-main		 Provides published, per-reviewed, quantitative models of biochemical and cellular systems.
Le NovE8re N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H, Li L, Sauro H, Schilstra M, Shapiro B, Snoep JL, Hucka M. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D689-91. PubMed PMID: 16381960; PubMed Central PMCID: PMC1347454.
2006
96
24 IPA - Ingenuity Pathways Analysis
http://www.ingenuity.com		 Curated database for biological network, created from large number of individually modelled relationship between the gene, proteins etc. Tool is available via Ingenuity pathway analysis suite.
Sreenivasaiah PK, Rani S, Cayetano J, Arul N, Kim DH. IPAVS: Integrated Pathway Resources, Analysis and Visualization System. Nucleic Acids Res. 2011 Dec 2. [Epub ahead of print] PubMed PMID: 22140115.
2011
96
Free trial available.
25 ResNet
http://www.ariadnegenomics.com/products/databases/ariadne-resnet		 Pathway database completely extracted from PubMed using MedScan and natural language processing tools.
Daraselia N, Yuryev A, Egorov S, Novichkova S, Nikitin A, Mazo I. Extracting human protein interactions from MEDLINE using a full-sentence parser. Bioinformatics. 2004 Mar 22;20(5):604-11. Epub 2004 Jan 22. PubMed PMID:15033866.
2004
96
26 SoyBase - USDA-ARS Soybean Genetics and Genome Database
http://soybase.ncgr.org		 Information about molecules and enzymes involved in soybean metabolic pathway.
Grant D, Nelson RT, Cannon SB, Shoemaker RC. SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Res. 2010 Jan;38(Database issue):D843-6. Epub 2009 Dec 14. PubMed PMID: 20008513; PubMed Central PMCID:PMC2808871.
2009
96
27 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
97
28 COPE - Cytokines and Cells Online Pathfinder Encyclopedia
http://www.copewithcytokines.de		 Encyclopedia of cytokines and related biological terms.
Ai-Aql ZS, Alagl AS, Graves DT, Gerstenfeld LC, Einhorn TA. Molecular mechanisms controlling bone formation during fracture healing and distraction osteogenesis. J Dent Res. 2008 Feb;87(2):107-18. Review. PubMed PMID: 18218835; PubMed Central PMCID: PMC3109437.
2008
97
29 EHMN - Edinburgh Human Metabolic Network
http://www.ehmn.bioinformatics.ed.ac.uk		 Human metabolic network manually reconstructed by integrating genome annotation information from different databases and metabolic reaction information from literature. The network contains nearly metabolic reactions, which were reorganized into human-specific metabolic pathways according to their functional relationships.
Ma H, Sorokin A, Mazein A, Selkov A, Selkov E, Demin O, Goryanin I. The Edinburgh human metabolic network reconstruction and its functional analysis. Mol Syst Biol. 2007;3:135. Epub 2007 Sep 18. PubMed PMID: 17882155; PubMed Central PMCID: PMC2013923.
2007
97
Registration required to access the resource.
30 HumanCyc
http://humancyc.org		 Describes human metabolic pathway and genome.
Romero P, Wagg J, Green ML, Kaiser D, Krummenacker M, Karp PD. Computational prediction of human metabolic pathways from the complete human genome. Genome Biol. 2005;6(1):R2. Epub 2004 Dec 22. PubMed PMID: 15642094; PubMed Central PMCID: PMC549063.
2004
97
31 MIM - Molecular Interaction Map
http://discover.nci.nih.gov/mim/index.jsp		 Uses clear, accurate, versatile graphical language to depict complex biological process.
Mewes HW, Amid C, Arnold R, Frishman D, GFCldener U, Mannhaupt G, MFCnsterkF6tter M, Pagel P, Strack N, StFCmpflen 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
97
32 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.
Cui Q, Lewis IA, Hegeman AD, Anderson ME, Li J, Schulte CF, Westler WM, Eghbalnia HR, Sussman MR, Markley JL. Metabolite identification via the Madison Metabolomics Consortium Database. Nat Biotechnol. 2008 Feb;26(2):162-4. PubMed PMID: 18259166.
2004
97
33 PathVisio 3
https://pathvisio.org/		 PathVisio 3 is an open-source pathway analysis and visualization tool that allows researchers to create, edit, and analyze biological pathways. It supports the integration of omics data (such as transcriptomics and proteomics) with pathway diagrams, enabling functional analysis and data visualization.
Kutmon, M., van Iersel, M. P., Bohler, A., Kelder, T., Nunes, N., Pico, A. R., & Evelo, C. T. (2015). PathVisio 3: an extendable pathway analysis toolbox. PLoS computational biology, 11(2), e1004085. https://doi.org/10.1371/journal.pcbi.1004085
2015
97
34 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 BD8, 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
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35 BioCarta
http://www.biocarta.com		 Gene interactions in dynamic graphical models, depicts molecular relationships.
Kluger Y, Tuck DP, Chang JT, Nakayama Y, Poddar R, Kohya N, Lian Z, Ben Nasr A, Halaban HR, Krause DS, Zhang X, Newburger PE, Weissman SM. Lineage specificity of gene expression patterns. Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6508-13. Epub 2004 Apr 19. PubMed PMID: 15096607; PubMed Central PMCID: PMC404075.
2004
98
36 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
98
37 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
98
38 i-GSEA4GWAS
http://gsea4gwas.psych.ac.cn		 Information on biochemical reactions.
Markowitz VM, Szeto E, Palaniappan K, Grechkin Y, Chu K, Chen IM, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Ivanova NN, Kyrpides NC. The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res. 2008 Jan;36(Database issue):D528-33. Epub 2007 Oct 12. PubMed PMID: 17933782; PubMed Central PMCID: PMC2238897.
2008
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39 IMG - Integrated Microbial Genomes
http://img.jgi.doe.gov		 Data management, analysis and annotation platform for all publicly available genomes.
Zhang K, Cui S, Chang S, Zhang L, Wang J. i-GSEA4GWAS: a web server for identification of pathways/gene sets associated with traits by applying an improved gene set enrichment analysis to genome-wide association study. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W90-5. Epub 2010 Apr 30. PubMed PMID: 20435672; PubMed Central PMCID: PMC2896119.
2007
98
40 MedicCyc
http://www.noble.org/mediccyc		 Pathway database for Medicago truncatula.
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
98
41 MetaCore
http://www.genego.com/metacore.php		 Database of molecular cellular pathways, and is designed to integrate data from different levels of cellular function.
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.
2007
98
License required to access the resource.
42 MMCD - Madison-Qingdao Metabolomics Consortium Database
http://mmcd.nmrfam.wisc.edu		 Resource of metabolic research based on the NMR spectroscopy and Mass spectometry.
Dunin-Horkawicz S, Czerwoniec A, Gajda MJ, Feder M, Grosjean H, Bujnicki JM. MODOMICS: a database of RNA modification pathways. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D145-9. PubMed PMID: 16381833; PubMed Central PMCID:PMC1347447.
2008
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43 MODOMICS
http://mmcd.nmrfam.wisc.edu		 Database of RNA modification pathways.
Gan HH, Fera D, Zorn J, Shiffeldrim N, Tang M, Laserson U, Kim N, Schlick T.RAG: RNA-As-Graphs database--concepts, analysis, and features. Bioinformatics.2004 May 22;20(8):1285-91. Epub 2004 Feb 12. PubMed PMID: 14962931.
2006
98
44 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
98
URL could not be retrieved (10/01/2012).
45 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
98
46 SMPDB - Small Molecule Pathway Database
http://www.smpdb.ca		 Contains metabolic pathways, disease pathways and drug action pathways. Shows the concentrations of various metabolites, proteins and genes.
Frolkis A, Knox C, Lim E, Jewison T, Law V, Hau DD, Liu P, Gautam B, Ly S, Guo AC, Xia J, Liang Y, Shrivastava S, Wishart DS. SMPDB: The Small Molecule Pathway Database. Nucleic Acids Res. 2010 Jan;38(Database issue):D480-7. Epub 2009 Nov 30. PubMed PMID: 19948758; PubMed Central PMCID: PMC2808928.
2009
98
47 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
98
48 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
98
49 BiGG - Biochemical Genetic and Genomic knowledgebase
http://bigg.ucsd.edu		 Knowledgebase of biochemically, genetically and genomically structured genome scale reconstructions, uses one standarad nomenclature allowing comparison across different species.
Thiele I, Hyduke DR, Steeb B, Fankam G, Allen DK, Bazzani S, Charusanti P, Chen FC, Fleming RM, Hsiung CA, De Keersmaecker SC, Liao YC, Marchal K, Mo ML, D6zdemir E, Raghunathan A, Reed JL, Shin SI, SigurbjF6rnsdF3ttir S, Steinmann J, Sudarsan S, Swainston N, Thijs IM, Zengler K, Palsson BO, Adkins JN, Bumann D. A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. BMC Syst Biol. 2011 Jan 18;5:8. PubMed PMID: 21244678; PubMed Central PMCID: PMC3032673.
2011
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50 Cancer Cell Map
http://cancer.cellmap.org/cellmap/		 Selected set of human cancer focused pathways.
Krogan, N. J., Lippman, S., Agard, D. A., Ashworth, A., & Ideker, T. (2015). The cancer cell map initiative: defining the hallmark networks of cancer. Molecular cell, 58(4), 690–698. https://doi.org/10.1016/j.molcel.2015.05.008
2015
99
51 ChemProt
http://www.cbs.dtu.dk/services/ChemProt		 Database of annotated and predicted chemical-protein interaction database.
Taboureau O, Nielsen SK, Audouze K, Weinhold N, EdsgE4rd D, Roque FS, Kouskoumvekaki I, Bora A, Curpan R, Jensen TS, Brunak S, Oprea TI. ChemProt: a disease chemical biology database. Nucleic Acids Res. 2011 Jan;39(Database issue):D367-72. Epub 2010 Oct 8. PubMed PMID: 20935044; PubMed Central PMCID:PMC3013776.
2010
99
52 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
99
53 DOQCS - Database of Quantitative Cellular Signaling
http://doqcs.ncbs.res.in		 Repository of models of signaling pathways and includes reactions, schemes, concentrations, rate constants, etc.
Sivakumaran S, Hariharaputran S, Mishra J, Bhalla US. The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks. Bioinformatics. 2003 Feb 12;19(3):408-15. PubMed PMID: 12584128.
2003
99
54 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
99
55 EcoCyc
http://ecocyc.org		 Database that describes the genome and metabolic pathways of E. coli K12MG1655.
Karp PD, Riley M, Paley SM, Pelligrini-Toole A. EcoCyc: an encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res. 1996 Jan 1;24(1):32-9. PubMed PMID: 8594595; PubMed Central PMCID: PMC145574.
1996
99
56 ERGO - ERGO Genome Analysis and Discovery System
http://www.ergo-light.com		 Curated database of genomic DNA with functional annotation and pathway information.
Overbeek R, Larsen N, Walunas T, D'Souza M, Pusch G, Selkov E Jr, Liolios K, Joukov V, Kaznadzey D, Anderson I, Bhattacharyya A, Burd H, Gardner W, Hanke P,KapatralV,Mikhailova N, Vasieva O, Osterman A, Vonstein V, Fonstein M, Ivanova N, Kyrpides N. The ERGO genome analysis and discovery system. Nucleic Acids Res. 2003 Jan 1;31(1):164-71. PubMed PMID: 12519973; PubMed Central PMCID: PMC165577.
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57 GenomeNet
https://www.genome.jp/		 GenomeNet serves as a crucial platform for researchers in molecular biology, genomics, and biotechnology, facilitating data integration and computational studies in life sciences.
Kanehisa, M., Goto, S., Kawashima, S., & Nakaya, A. (2002). The KEGG databases at GenomeNet. Nucleic acids research, 30(1), 42–46. https://doi.org/10.1093/nar/30.1.42
2002
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58 Graphcrunch
http://www.ics.uci.edu/~bio-nets/graphcrunch		 Software for analyzing and modeling large biological networks.
Milenkovic T, Lai J, Przulj N. GraphCrunch: a tool for large network analyses.BMC Bioinformatics. 2008 Jan 30;9:70. PubMed PMID: 18230190; PubMed Central PMCID: PMC2275247.
2008
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URL: temporarily unavailable (10/01/2012).
59 HCPIN - Human Cancer Protein Interaction Network
http://nesg.org:9090/HCPIN		 Interaction among the proteins associated with cancer.
Huang YJ, Hang D, Lu LJ, Tong L, Gerstein MB, Montelione GT. Targeting the human cancer pathway protein interaction network by structural genomics. Mol Cell Proteomics. 2008 Oct;7(10):2048-60. Epub 2008 May 18. PubMed PMID: 18487680; PubMed Central PMCID: PMC2559933.
2008
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60 IntEnz - Integrated relational Enzyme database
http://www.ebi.ac.uk/intenz/index.jsp		 The most up to date version of enzyme nomenclature.
Letunic I, Yamada T, Kanehisa M, Bork P. iPath: interactive exploration of biochemical pathways and networks.Trends Biochem Sci. 2008 Mar;33(3):101-3. Epub 2008 Feb 13. PubMed PMID: 18276143.
2004
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61 KaPPA-View4
http://kpv.kazusa.or.jp/kpv4		 Metabolic pathway database to better understand the metabolic regulation and derive hypothesis based on the data available from the transcriptome, metabolome and co-expression of genes.
Kohn KW. Molecular interaction map of the mammalian cell cycle control and DNA repair systems. Mol Biol Cell. 1999 Aug;10(8):2703-34. Review. PubMed PMID:10436023; PubMed Central PMCID: PMC25504.
2011
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62 KnowledgeEditor
http://gscope.gsc.riken.go.jp		 Graphical workbench to model biomolecular network graphs and analyze biological pathways based on microarray data. The modeled network data created, are represented by SRML, and can be published via the internet with the help of plug-in module 'GSCope'.
Schmelzer K, Fahy E, Subramaniam S, Dennis EA. The lipid maps initiative in lipidomics. Methods Enzymol. 2007;432:171-83. PubMed PMID: 17954217.
2003
99
URL could not be retrieved (10/01/2012).
63 Malaria Parasite Metabolic Pathways
http://sites.huji.ac.il/malaria		 Information on malaria biology, biochemistry and physiology.
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.
2006
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64 MANET - Molecular Ancestry Network
http://www.manet.uiuc.edu		 Characterize and describe quantitatively the networks of molecular interactions in biological systems.
Urbanczyk-Wochniak E, Sumner LW. MedicCyc: a biochemical pathway database for Medicago truncatula. Bioinformatics. 2007 Jun 1;23(11):1418-23. Epub 2007 Mar 7. PubMed PMID: 17344243.
2006
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65 METANETTER
http://compbio.dcs.gla.ac.uk		 Inferring networks from high resolution mass spectrometry.
Pinney JW, Shirley MW, McConkey GA, Westhead DR. metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella. Nucleic Acids Res. 2005 Mar 3;33(4):1399-409. Print 2005. PubMed PMID: 15745999; PubMed Central PMCID:PMC552966.
2007
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66 METAPATH
http://scopes.biologie.hu-berlin.de/index.php?m=path		 Calculation of minimal synthesis pathway.
Pfeiffer T, SE1nchez-Valdenebro I, NuF1o JC, Montero F, Schuster S. METATOOL: for studying metabolic networks. Bioinformatics. 1999 Mar;15(3):251-7. PubMed PMID: 10222413.
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67 metaSHARK
http://bioinformatics.leeds.ac.uk/shark		 Metabolic reconstruction information for specific organisms.
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.
2005
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68 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, M.P., Charles, H., Sagot, M.F. and Jourdan, F., 2010. MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks. Nucleic acids research, 38(suppl_2), pp.W132-W137.
2010
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69 Millipore Pathways
http://www.millipore.com/pathways/pw/pathways		 Browse for pathways with respect to disease areas.
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
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70 MiMI - Michigan Molecular Interactions
http://mimi.ncibi.org/MimiWeb/main-page.jsp		 Contains pathway diagrams from KEGG and Reactome.
Ulrich LE, Zhulin IB. MiST: a microbial signal transduction database. Nucleic Acids Res. 2007 Jan;35(Database issue):D386-90. Epub 2006 Nov 28. PubMed PMID:17135192; PubMed Central PMCID: PMC1747179.
2006
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71 MouseCyc
http://mousecyc.jax.org		 Database of curated biochemical pathways data from the laboratory mouse that can be integrated with the functional and phenotypic data from MGI.
Evsikov, A.V., Dolan, M.E., Genrich, M.P., Patek, E. and Bult, C.J., 2009. MouseCyc: a curated biochemical pathways database for the laboratory mouse. Genome Biology, 10, pp.1-10.
2009
99
URL could not be retrieved (10/01/2012).
72 MRAD - Metabolic Reaction Analysis Database
http://capb.dbi.udel.edu/whisler		 Database based on the entity relationship model developed with an aim to use biological information retreived from databases to build flux balance models.
BrohE9e S, Faust K, Lima-Mendez G, Vanderstocken G, van Helden J. Network Analysis Tools: from biological networks to clusters and pathways. Nat Protoc. 2008;3(10):1616-29. PubMed PMID: 18802442.
2003
99
URL could not be retrieved (10/01/2012).
73 NetSlim
http://www.netpath.org/netslim		 A public resource of high-confidence signaling pathway maps generated from NetPath pathway reactions. NetSlim maps are freely available for download in .GPML, .GenMAPP, .PDF and .SVG formats.
McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes S, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman A, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko O, Xia F, Zinner J, Overbeek R, Stevens R. The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53.Epub 2006 Dec 1. PubMed PMID: 17145713; PubMed Central PMCID: PMC1751540.
2011
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74 NetworKIN
http://networkin.info		 Predicting the in vivo kinase substrate relationships, that augments consensus motifs with context to kinases and phosphoproteins.
Barakat M, Ortet P, Jourlin-Castelli C, Ansaldi M, ME9jean V, Whitworth DE. P2CS: a two-component system resource for prokaryotic signal transduction research. BMC Genomics. 2009 Jul 15;10:315. PubMed PMID: 19604365 ; PubMed Central PMCID: PMC2716373.
2007
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75 PathBank
https://pathbank.org/		 PathBank is a comprehensive database of human metabolic, signaling, and disease-related pathways. It integrates data from multiple sources, including metabolomics, proteomics, transcriptomics, and genomics, to provide detailed pathway maps and molecular interactions.
Wishart, D. S., Li, C., Marcu, A., Badran, H., Pon, A., Budinski, Z., Patron, J., Lipton, D., Cao, X., Oler, E., Li, K., Paccoud, M., Hong, C., Guo, A. C., Chan, C., Wei, W., & Ramirez-Gaona, M. (2020). PathBank: a comprehensive pathway database for model organisms. Nucleic acids research, 48(D1), D470–D478. https://doi.org/10.1093/nar/gkz861
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76 PathPred - Pathway Prediction server
http://www.genome.jp/tools/pathpred		 Enzyme catalyzed metabolic pathway prediction server.
Moriya Y, Shigemizu D, Hattori M, Tokimatsu T, Kotera M, Goto S, Kanehisa M.PathPred: an enzyme-catalyzed metabolic pathway prediction server. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W138-43. Epub 2010 Apr 30. PubMed PMID:20435670; PubMed Central PMCID: PMC2896155.
2010
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77 Pathway explorer
https://pathwayexplorer.genome.tugraz.at		 For visualizing high-throughput expression data on biological pathways.
Mlecnik B, Scheideler M, Hackl H, Hartler J, Sanchez-Cabo F, Trajanoski Z. PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W633-7.PubMed PMID: 15980551; PubMed Central PMCID: PMC1160152.
2005
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78 Pathway Miner - Classify and Extract Network of Associated Genes/Proteins based on Pathways
http://www.biorag.org/pathway.html		 Extract networks of associated genes or proteins based on the pathways.
Pandey R, Guru RK, Mount DW. Pathway Miner: extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data. Bioinformatics. 2004 Sep 1;20(13):2156-8. Epub 2004 May 14. PubMed PMID: 15145817.
2004
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Requires JAVA +5.0.
79 PATIKA - Pathway Analysis Tool for Integration and Knowledge Acquisition
http://www.patika.org		 A combination of Java pathway modeling tool and an object oriented pathway database.
Demir E, Babur O, Dogrusoz U, Gursoy A, Nisanci G, Cetin-Atalay R, Ozturk M. PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways. Bioinformatics. 2002 Jul;18(7):996-1003. PubMed PMID: 12117798.
2002
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80 PATRIC - PathoSystems Resource Integration Center
http://patric.vbi.vt.edu		 Pathway resources for bacteria and viruses.
Snyder EE, Kampanya N, Lu J, Nordberg EK, Karur HR, Shukla M, Soneja J, Tian Y, Xue T, Yoo H, Zhang F, Dharmanolla C, Dongre NV, Gillespie JJ, Hamelius J, Hance M, Huntington KI, Jukneliene D, Koziski J, Mackasmiel L, Mane SP, Nguyen V, Purkayastha A, Shallom J, Yu G, Guo Y, Gabbard J, Hix D, Azad AF, Baker SC, Boyle SM, Khudyakov Y, Meng XJ, Rupprecht C, Vinje J, Crasta OR, Czar MJ, Dickerman A, Eckart JD, Kenyon R, Will R, Setubal JC, Sobral BW. PATRIC: the VBI PathoSystems Resource Integration Center. Nucleic Acids Res. 2007 Jan;35(Database issue):D401-6. Epub 2006 Nov 16. PubMed PMID: 17142235; PubMed Central PMCID: PMC1669763.
2006
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81 PlantCyc
http://www.plantcyc.org		 Contains pathways, genes, catalytic enzymes and compounds from many different plant species.
Zhang P, Dreher K, Karthikeyan A, Chi A, Pujar A, Caspi R, Karp P, Kirkup V, Latendresse M, Lee C, Mueller LA, Muller R, Rhee SY. Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants. Plant Physiol. 2010 Aug;153(4):1479-91. Epub 2010 Jun 3. PubMed PMID: 20522724; PubMed Central PMCID:PMC2923894.
2010
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82 RegPhos
http://RegPhos.mbc.nctu.edu.tw		 Input a group of genes or proteins to explore the phosphorylation network and the association with the subcellular organelles.
Lee TY, Bo-Kai Hsu J, Chang WC, Huang HD. RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans. Nucleic Acids Res.2011 Jan;39(Database issue):D777-87. Epub 2010 Oct 30. PubMed PMID: 21037261;PubMed Central PMCID: PMC3013804.
2010
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83 REPAIRtoire - A database of DNA repair pathways
http://repairtoire.genesilico.pl		 Contains components involved in all kinds of repair mechanisms of cellular DNA lesions.
Milanowska K, Krwawicz J, Papaj G, Kosinski J, Poleszak K, Lesiak J, Osinska E, Rother K, Bujnicki JM. REPAIRtoire--a database of DNA repair pathways. Nucleic Acids Res. 2011 Jan;39(Database issue):D788-92. Epub 2010 Nov 4. PubMed PMID:21051355; PubMed Central PMCID: PMC3013684.
2010
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84 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
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85 RGD - Rat Genome Database
http://rgd.mcw.edu/wg/pathway		 Integrates pathways from KEGG and Reactome and pathways curated from literature including regulatory and signaling pathways.
Twigger SN, Shimoyama M, Bromberg S, Kwitek AE, Jacob HJ; RGD Team. The Rat Genome Database, update 2007--easing the path from disease to data and back again. Nucleic Acids Res. 2007 Jan;35(Database issue):D658-62. Epub 2006 Dec 6. PubMed PMID: 17151068; PubMed Central PMCID: PMC1761441.
2007
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86 RiceCyc - Rice metabolic pathways
http://www.gramene.org/pathway/ricecyc.html		 Information on metabolic pathways in rice.
Jaiswal P, Ni J, Yap I, Ware D, Spooner W, Youens-Clark K, Ren L, Liang C, Zhao W, Ratnapu K, Faga B, Canaran P, Fogleman M, Hebbard C, Avraham S, Schmidt S, Casstevens TM, Buckler ES, Stein L, McCouch S. Gramene: a bird's eye view of cereal genomes. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D717-23. PubMed PMID: 16381966; PubMed Central PMCID: PMC1347516.
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87 Allows system level analysis using the network of intracellular signaling pathways.
KorcsmE1ros T, Farkas IJ, Szalay MS, RovF3 P, Fazekas D, SpirF3 Z, BF6de 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
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88 T1DBase
http://t1dbase.org		 Includes annotated genomic sequences for suspected T1D susceptibility regions, microarray data, functional annotation of the genes active in beta cells and datasets from literature useful for system biology studies.
Hulbert EM, Smink LJ, Adlem EC, Allen JE, Burdick DB, Burren OS, Cassen VM, Cavnor CC, Dolman GE, Flamez D, Friery KF, Healy BC, Killcoyne SA, Kutlu B, Schuilenburg H, Walker NM, Mychaleckyj J, Eizirik DL, Wicker LS, Todd JA, Goodman N. T1DBase: integration and presentation of complex data for type 1 diabetes research. Nucleic Acids Res. 2007 Jan;35(Database issue):D742-6. Epub 2006 Dec 14. Erratum in: Nucleic Acids Res. 2007;35(18):6338. Cassen, Victor M [added].PubMed PMID: 17169983; PubMed Central PMCID: PMC1781218.
2006
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89 TECR - Thermodynamics of Enzyme-Catalyzed Reactions
http://xpdb.nist.gov/enzyme_thermodynamics		 Thermodynamic data of enzyme catalyzed reactions.
Goldberg RN, Tewari YB, Bhat TN. Thermodynamics of enzyme-catalyzed reactions--a database for quantitative biochemistry. Bioinformatics. 2004 Nov 1;20(16):2874-7. Epub 2004 May 14. PubMed PMID: 15145806.
2004
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90 TRANSPATH
http://www.biobase-international.com/pages/?id=39		 Signaling pathways linked with transcription factors.
Krull M, Voss N, Choi C, Pistor S, Potapov A, Wingender E. TRANSPATH: an integrated database on signal transduction and a tool for array analysis. Nucleic Acids Res. 2003 Jan 1;31(1):97-100. PubMed PMID: 12519957; PubMed Central PMCID: PMC165536.
2003
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URL could not be retrieved (10/01/2012).
91 VirHostNet
http://pbildb1.univ-lyon1.fr/virhostnet/login.php		 Knowledgebase system for curation, analysis and management of virus-host molecular interactions.
Navratil V, de Chassey B, Meyniel L, Delmotte S, Gautier C, AndrE9 P, LotteauV, Rabourdin-Combe C. VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks. Nucleic Acids Res.2009 Jan ; 37(Database issue):D661-8. Epub 2008 Nov 4. PubMed PMID: 18984613;PubMed Central PMCID: PMC2686459.
2009
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92 WIT - What Is There?
http://wit.mcs.anl.gov/WIT2		 Metabolic reconstruction for sequenced genomes.
Overbeek R, Larsen N, Pusch GD, D'Souza M, Selkov E Jr, Kyrpides N, Fonstein M, Maltsev N, Selkov E. WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res. 2000 Jan 1;28(1):123-5. PubMed PMID: 10592199; PubMed Central PMCID: PMC102471.
2000
99
URL could not be retrieved (10/01/2012).
93 WPS - WholePathwayScope
http://www.abcc.ncifcrf.gov/wps/wps_index		 For pathway-based analysis of high throughput data obtained fron microarray or proteomics.
Yi M, Horton JD, Cohen JC, Hobbs HH, Stephens RM. WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data. BMC Bioinformatics. 2006 Jan 19;7:30. PubMed PMID: 16423281; PubMed Central PMCID: PMC1388242.
2006
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94 aMAZE
http://www.amaze.ulb.ac.be		 Represents and analyze molecular interactions and cellular processes, implements data-model for associating individual biological entities and interactions into large complex networks.
van Helden J, Naim A, Mancuso R, Eldridge M, Wernisch L, Gilbert D, Wodak SJ. Representing and analysing molecular and cellular function using the computer. Biol Chem. 2000 Sep-Oct;381(9-10):921-35. Review. PubMed PMID: 11076023.
2000
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URL could not be retrieved (10/01/2012).
95 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
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96 ArrayXpath
http://www.snubi.org/software/ArrayXPath		 Mapping and visualizing microarray gene expression data for integrated biological pathways using "scalable vector graphics".
Chung HJ, Kim M, Park CH, Kim J, Kim JH. ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W460-4. PubMed PMID: 15215430; PubMed Central PMCID: PMC441614.
2004
100
License required to access the resource.
97 BBID - Biological Biochemical Image Database
http://bbid.grc.nia.nih.gov		 Accessible relational database of archived images from research articles describing the regulatory networks in eukaryotes.
Becker KG, White SL, Muller J, Engel J. BBID: the biological biochemical image database. Bioinformatics. 2000 Aug;16(8):745-6. PubMed PMID: 11099263.
2000
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98 BiologicalNetworks
http://biologicalnetworks.org		 Curated and publicly contributed data for several thousands of eukaryotic, prokaryotic and viral organisms.
Baitaluk M, Qian X, Godbole S, Raval A, Ray A, Gupta A. PathSys: integrating molecular interaction graphs for systems biology. BMC Bioinformatics. 2006 Feb 7;7:55. PubMed PMID: 16464251; PubMed Central PMCID: PMC1409799.
2006
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99 Bionemo
http://bionemo.bioinfo.cnio.es		 Biodegradation network database.
Carbajosa G, Trigo A, Valencia A, Cases I. Bionemo: molecular information on biodegradation metabolism. Nucleic Acids Res. 2009 Jan;37(Database issue):D598-602. Epub 2008 Nov 5.PubMed PMID: 18986994; PubMed Central PMCID:PMC2686592.
2008
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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
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101 BIOPYDB - BIOchemical PathwaY DataBase
http://biopydb.ncl.res.in/		 BIOPYDB offers tools for Topological, Logical, and Dynamic analyses, automated pathway image reconstruction, cross-referencing with other databases, and advanced search capabilities.
Chowdhury, S., Sinha, N., Ganguli, P., Bhowmick, R., Singh, V., Nandi, S., & Sarkar, R. R. (2018). BIOPYDB: A Dynamic Human Cell Specific Biochemical Pathway Database with Advanced Computational Analyses Platform. Journal of integrative bioinformatics, 15(3), 20170072. https://doi.org/10.1515/jib-2017-0072
2018
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102 BioSilico
http://biosilico.kaist.ac.kr		 Combination of heterogenous pathway databases, search and analysis of metabolic pathways.
Hou BK, Kim JS, Jun JH, Lee DY, Kim YW, Chae S, Roh M, In YH, Lee SY. BioSilico: an integrated metabolic database system. Bioinformatics. 2004 Nov22;20(17):3270-2. Epub 2004 Jun 16. PubMed PMID: 15201189.
2004
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103 BSD - Biodegradability Strain Database
http://bsd.cme.msu.edu		 Information on the biodegradation pathways based on the strain or the substance involved.
Urbance JW, Cole J, Saxman P, Tiedje JM. BSD: the Biodegradative Strain Database. Nucleic Acids Res. 2003 Jan 1;31(1):152-5. PubMed PMID: 12519970; PubMed Central PMCID: PMC165479.
2003
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104 Caleydo
http://www.icg.tugraz.at/project/caleydo		 Understanding relationship of pathways and altered expression of these components in disease condition.
Streit M, Lex A, Kalkusch M, Zatloukal K, Schmalstieg D. Caleydo: connecting pathways and gene expression. Bioinformatics. 2009 Oct 15;25(20):2760-1. Epub 2009 Jul 20. PubMed PMID: 19620095; PubMed Central PMCID: PMC2759551.
2009
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105 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.
106 CellML Model Repository
http://models.cellml.org/cellml		 Supports both quantitative and qualitative pathway models.
Nickerson D, Stevens C, Halstead M, Hunter P, Nielsen P. Toward a curated CellML model repository. Conf Proc IEEE Eng Med Biol Soc. 2006;1:4237-40. PubMed PMID: 17947072.
2006
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107 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
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108 CSNDB - Cell Signaling Networks Database
http://www.vivo.library.cornell.edu/display/individual5061		 Signaling pathways compiled as binary relationship of biomolecules and represented by graphs drawn automatically. Constructed on ACEDB and inference engine CLIPS, has linkage to TRANSFAC.
Igarashi T, Kaminuma T. Development of a cell signaling networks database. Pac Symp Biocomput. 1997:187-97. PubMed PMID: 9390291.
1997
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109 CST - Cell Signaling Technology Pathway Database
http://www.cellsignal.com		 Showcases cell signaling technology phospho-antibody products.
Watkins GR. Constructing the CST default client response database. Issues.1995;16(1):9-10. PubMed PMID: 7775171.
1995
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110 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
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URL: temporarily unavailable (10/01/2012).
111 DSM - Dynamic Signaling Maps
http://www.hippron.com/hippron		 Web based software for creating custom pathway diagrams, using symbolic language.
Not available
100
URL: temporarily unavailable (10/01/2012).
112 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).
113 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.
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114 GeneNet - Gene Networks
http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet		 Visualization and simulation of gene network dynamics.
Kolpakov FA, Ananko EA. Interactive data input into the GeneNet database.Bioinformatics. 1999 Jul-Aug;15(7-8):713-4. PubMed PMID: 10487877.
1999
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115 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).
116 GEPAT - Genome Expression Pathway Analysis Tool
http://gepat.sourceforge.net		 Integrated analysis of transcriptome data under the proteome, genomic and metabolomic context.
Weniger M, Engelmann JC, Schultz J. Genome Expression Pathway Analysis Tool--analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context. BMC Bioinformatics. 2007 Jun 2;8:179. PubMed PMID: 17543125; PubMed Central PMCID: PMC1896182.
2007
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117 GLAMM - Genome-Linked Application for Metabolic Maps
http://glamm.lbl.gov		 Visualizing and reconstructing metabolic networks from annotated genome data.
Bates JT, Chivian D, Arkin AP. GLAMM: Genome-Linked Application for Metabolic Maps. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W400-5. Epub 2011 May 29.PubMed PMID: 21624891 ; PubMed Central PMCID: PMC3125797.
2011
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118 GOAPhAR - Gene Ontology, Annotations and Pathways for Array Research
http://bioinformatics.kumc.edu/goaphar		 Provides information about the gene identifiers and gives the list of signaling and metabolic pathways associated with them.
Mathur S, Visvanathan M, Svojanovsky S, Yoo B, Srinivas AB, Lushington GH, Smith PG. GOAPhAR: An Integrative Discovery Tool for Annotation, Pathway Analysis. Open Bioinforma J. 2009 Jan 1;3:26-30. PubMed PMID: 21132056; PubMed Central PMCID: PMC2995274.
2009
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119 GOLD.db - Genomics of Lipid-associated Disorders
https://gold.tugraz.at/Main.jsp		 Integrated information on function and properties of genes and proteins that are relevant in biology, disease diagnosis and management.
Hackl H, Maurer M, Mlecnik B, Hartler J, Stocker G, Miranda-Saavedra D, Trajanoski Z. GOLD.db: genomics of lipid-associated disorders database. BMC Genomics. 2004 Dec 10;5(1):93. PubMed PMID: 15588328; PubMed Central PMCID: PMC544894.
2004
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120 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
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121 GS2PATH
http://array.kobic.re.kr:8080/arrayport/gs2path		 Provides an estimation of gene set enrichment in GO terms and explores the functional relationship using the biological pathways.
Yang JO, Charny P, Lee B, Kim S, Bhak J, Woo HG. GS2PATH: a web-based integrated analysis tool for finding functional relationships using gene ontology and biochemical pathway data. Bioinformation. 2007 Dec 30;2(5):194-6. PubMed PMID: 18305828; PubMed Central PMCID: PMC2241924.
2007
100
URL could not be retrieved (10/01/2012).
122 GSCope3
http://omicspace.riken.jp/osml		 Tool for ranking biological pathways with SOM clustered microarray data.
Hasegawa Y, Seki M, Mochizuki Y, Heida N, Hirosawa K, Okamoto N, Sakurai T, Satou M, Akiyama K, Iida K, Lee K, Kanaya S, Demura T, Shinozaki K, Konagaya A,Toyoda T. A flexible representation of omic knowledge for thorough analysis of microarray data. Plant Methods. 2006 Mar 2;2:5. PubMed PMID: 16509996; PubMed Central PMCID: PMC1421397.
2006
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123 GTDB - Glycosylation Pathways Database
https://www.biosino.org/gtdb/		 Exclusively for glycosylation pathways.
Chenfen Zhou, Qingwei Xu, Sheng He, Wei Ye, Ruifang Cao, Pengyu Wang, Yunchao Ling, Xing Yan, Qingzhong Wang, Guoqing Zhang, GTDB: an integrated resource for glycosyltransferase sequences and annotations, Database, Volume 2020, 2020, baaa047, https://doi.org/10.1093/database/baaa047
2020
100
URL could not be retrieved (10/01/2012).
124 Hedgehog Signaling Pathway Database
http://hedgehog.sfsu.edu		 Information on hedgehog signaling pathway, pathway model diagrams, list of genes, expression in tissues and mutation in diseases.
Hervold K, Martin A, Kirkpatrick RA, Mc Kenna PF, Ramirez-Weber FA. Hedgehog Signaling Pathway Database: a repository of current annotation efforts and resources for the Hh research community. Nucleic Acids Res. 2007 Jan;35(Database issue):D595-8. Epub 2006 Dec 6. PubMed PMID: 17151082; PubMed Central PMCID: PMC1781108.
2007
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Service Temporarily Unavailable
125 hiPathDB - human-integrated pathway database
http://hiPathDB.kobic.re.kr		 A pathway database that provides two different types of integration: pathway-level integration, a simple collection of individual pathways and entity-level integration, unified pathway by merging common components. The database combines the curated human pathway data of NCI-Nature PID, Reactome, BioCarta and KEGG.
Yu N, Seo J, Rho K, Jang Y, Park J, Kim WK, Lee S. hiPathDB: a human-integrated pathway database with facile visualization. Nucleic Acids Res. 2011 Nov 28. [Epub ahead of print] PubMed PMID: 22123737.
2011
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126 HPD - Human Pathway Database
http://bio.informatics.iupui.edu/HPD		 Gives the pathway-pathway similarity matrix, pathway-protein association matrix.
Chowbina SR, Wu X, Zhang F, Li PM, Pandey R, Kasamsetty HN, Chen JY. HPD: an online integrated human pathway database enabling systems biology studies. BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S5. PubMed PMID: 19811689.
2009
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127 IBRENA - In silico Biochemical Reaction Network Analysis
http://www.eng.buffalo.edu/~neel/ibrena		 Identification of pathways or genes associated with a trait.
NitschkE9 P, Guerdoux-Jamet P, Chiapello H, Faroux G, HE9naut C, HE9naut A, Danchin A. Indigo: a World-Wide-Web review of genomes and gene functions. FEMS Microbiol Rev. 1998 Oct;22(4):207-27. Review. PubMed PMID: 9862121.
2010
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128 Ingeneue - Gene network simulation software
http://rusty.fhl.washington.edu/ingeneue		 Software for synthesizing molecular genetic data into models of genetic networks. The user can quickly turn a map of a genetic network into a dynamical model consisting of a set of ordinary differential equations.
Fukuda K, Takagi T. Knowledge representation of signal transduction pathways. Bioinformatics. 2001 Sep;17(9):829-37. PubMed PMID: 11590099.
2002
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129 InnateDB - A Knowledge Resource for Innate Immunity Interactions and Pathways
http://www.innatedb.ca		 Text mining, pathway diagram tools, interaction or functional association prediction.
Liu G, Neelamegham S. In silico Biochemical Reaction Network Analysis (IBRENA): a package for simulation and analysis of reaction networks. Bioinformatics. 2008 Apr 15;24(8):1109-11. Epub 2008 Feb 28. PubMed PMID:18310056.
2008
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130 INOH - Integrating Network Objects with Hierarchies
http://www.inoh.org		 Pathway database of model organisms including mouse, rat, human and others.
Yamamoto, S., Kushida, T., Ono, N., Yamagata, Y., Takagi, T. and Fukuda, K.I., 2003. INOH: A Textual Knowledge Based Pathway Database. Genome Informatics, 14, pp.679-680.
2003
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131 iPath
http://escience.invitrogen.com/ipath		 Contains interactive maps of signaling and metabolic pathway, showcases invitrogen products.
Nicholson DE. The evolution of the IUBMB-Nicholson maps. IUBMB Life. 2000 Dec;50(6):341-4. PubMed PMID: 11327304.
2008
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URL: temporarily unavailable (10/01/2012).
132 iPAVS - Integrated Pathway Resources, Analysis and Visualization System
http://ipavs.cidms.org		 An integrated biological pathway database to support pathway discovery in the fields of proteomics, transcriptomics, metabolomics and systems biology. It provides access to expert-curated pathways of specific biological contexts related to cell types, tissues, organs and diseases. It includes metabolic, signaling and disease-related pathways, drug-action pathways, etc., pooled from other pathway resources.
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.
2011
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133 IUBMB-Nicholson Minimaps
http://www.iubmb-nicholson.org		 Collection of metabolic pathway diagrams.
Sakurai N, Ara T, Ogata Y, Sano R, Ohno T, Sugiyama K, Hiruta A, Yamazaki K, Yano K, Aoki K, Aharoni A, Hamada K, Yokoyama K, Kawamura S, Otsuka H, Tokimatsu T, Kanehisa M, Suzuki H, Saito K, Shibata D. KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data. Nucleic Acids Res. 2011 Jan;39(Database issue):D677-84. Epub 2010 Nov 19. PubMed PMID: 21097783;PubMed Central PMCID: PMC3013809.
2000
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134 KMIM - Kohn Molecular Interaction Maps
http://discover.nci.nih.gov/mim/kohnk/kohnk.jsp		 Provides two diagrams as a symbolic representation of signaling pathways.
Doyle MA, MacRae JI, De Souza DP, Saunders EC, McConville MJ, Likic VA. LeishCyc: a biochemical pathways database for Leishmania major. BMC Syst Biol. 2009 Jun 5;3:57. PubMed PMID: 19497128; PubMed Central PMCID: PMC2700086.
1999
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135 LeishCyc - biochemical pathways database for Leishmania major
http://www.leishcyc.org		 A biochemical pathways database for Leishmania major. It describes Leishmania major genes, gene products, metabolites, their relationships and biochemical organization into metabolic pathways. It serves as a tool for analysis, interpretation, and visualization of Leishmania Omics data (transcriptomics, proteomics, metabolomics) in the context of metabolic pathways.
Nagasaki M, Saito A, Fujita A, Tremmel G, Ueno K, Ikeda E, Jeong E, Miyano S. Systems biology model repository for macrophage pathway simulation. Bioinformatics. 2011 Jun 1;27(11):1591-3. Epub 2011 Apr 19. PubMed PMID: 21505034.
2009
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136 MACPAK - Simulatable Macrophage Pathway Knowledgebase
http://macpak.csml.org		 Focused on LPS-induced macrophage signaling pathways, contains pathways for genes derived from many reports.
Kim HS, Mittenthal JE, Caetano-AnollE9s G. MANET: tracing evolution of protein architecture in metabolic networks. BMC Bioinformatics. 2006 Jul 19;7:351. PubMed PMID: 16854231; PubMed Central PMCID: PMC1559654.
2011
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137 MetaCrop
http://pgrc-35.ipk-gatersleben.de/pls/htmldb_pgrc/f?p=269:111:802960176267400		 Hand-curated information of major metabolic pathways in crops.
Lee DY, Yun H, Park S, Lee SY. MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis. Bioinformatics.2003 Nov 1;19(16):2144-6. PubMed PMID: 14594721.
2007
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138 MetaCyc - Metabolic Pathway Database
http://metacyc.org		 Contains pathways from different organisms.
Ogata H, Claverie JM. Metagrowth: a new resource for the building of metabolic hypotheses in microbiology. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D321-4. PubMed PMID: 15608207; PubMed Central PMCID: PMC539996.
2004
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139 MetaFluxNet
http://metafluxnet.kaist.ac.kr		 Quantitative in silico simulation of metabolic pathways.
Hofmeyr JH, van der Merwe KJ. METAMOD: software for steady-state modelling and control analysis of metabolic pathways on the BBC microcomputer. Comput Appl Biosci. 1986 Dec;2(4):243-9. PubMed PMID: 3450367.
2003
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140 Metagrowth
http://igs-server.cnrs-mrs.fr/axenic		 Study of culture condition of obligate parasitic bacteria.
Jourdan F, Breitling R, Barrett MP, Gilbert D. MetaNetter: inference and visualization of high-resolution metabolomic networks. Bioinformatics. 2008 Jan 1;24(1):143-5. Epub 2007 Nov 14. PubMed PMID: 18003642.
2005
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141 METAMOD
http://metamod.org		 Microcomputer-based software for steady-state modelling and control analysis of model metabolic pathways. The package has two programs: METADEF, to define the pathway in terms of reactions, rate equations and initial concentrations of metabolites and METACAL, to calculate the steady-state concentrations and fluxes.
Handorf T, EbenhF6h 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.
1986
100
License required to access the resource.
142 METATOOL
http://pinguin.biologie.uni-jena.de/bioinformatik/networks		 For detection of independent pathways from substrates to products and for the disassembly of large biochemical networks to subnets.
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.
1999
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143 MetNetDB - MetNet (Metabolic Network Exchange) database
http://www.metnetdb.org/MetNet_db.htm		 Information on metabolic and regulatory interactions in Arabidopsis.
Aladjem MI, Pasa S, Parodi S, Weinstein JN, Pommier Y, Kohn KW. Molecular interaction maps--a diagrammatic graphical language for bioregulatory networks. Sci STKE. 2004 Feb 24;2004(222):pe8. Review. PubMed PMID: 14997004.
2003
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144 MiST - Microbial Signal Transduction database
http://genomics.ornl.gov/mist		 Signal transduction proteins in bacterial and archeal organisms.
Sanguinetti G, Noirel J, Wright PC. MMG: a probabilistic tool to identify submodules of metabolic pathways. Bioinformatics. 2008 Apr 15;24(8):1078-84. Epub 2008 Feb 21. PubMed PMID: 18292114.
2007
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145 MMG - Mixture Model on Graphs
http://staffwww.dcs.shef.ac.uk/people/GONEAWAY/software.html		 Probabilistic tool to identify the submodules of metabolic pathways.
Li J, Ning Y, Hedley W, Saunders B, Chen Y, Tindill N, Hannay T, Subramaniam S. The Molecule Pages database. Nature. 2002 Dec 12;420(6916):716-7. PubMed PMID:12478304.
2008
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URL could not be retrieved (10/01/2012).
146 Molecule Pages
http://www.signaling-gateway.org		 Cell signaling database designed to facilitate navigation of complex world of research.
Lall R, Gao G, Dhurjati P, Edwards J. MRAD: Metabolic reaction analysis database--an entity-relationship approach. J Mol Microbiol Biotechnol.2003;6(1):12-8. PubMed PMID: 14593249.
2002
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147 Monod - Modeler's Notebook and Datastore
http://monod.molsci.org		 Collaborative tool for construction of mathematical models of biological processes.
Soergel, D., George, B., Morgan-Linial, R., Brent, R. and Endy, D., 2003. Monod, a tool to support collaborative modeling of biological processes. Unpublished manuscript, Molecular Sciences Institute, Berkeley, California, USA.
2003
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148 MPB - Metabolic Pathways of Biochemistry
http://dwb4.unl.edu/chem/chem869p/chem869plinks/www.gwu.edu/~mpb		 Shows some of the imporatant pathway associated with human biochemistry.
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149 NetBiochem
http://library.med.utah.edu/NetBiochem/NetWelco.htm		 Primarily an education resource to teach the biochemical pathways.
Raju R, Nanjappa V, Balakrishnan L, Radhakrishnan A, Thomas JK, Sharma J, Tian M, Palapetta SM, Subbannayya T, Sekhar NR, Muthusamy B, Goel R, Subbannayya Y, Telikicherla D, Bhattacharjee M, Pinto SM, Syed N, Srikanth MS, Sathe GJ, Ahmad S, Chavan SN, Kumar GS, Marimuthu A, Prasad TS, Harsha HC, Rahiman BA, Ohara O, Bader GD, Sujatha Mohan S, Schiemann WP, Pandey A. NetSlim: high-confidence curated signaling maps. Database (Oxford). 2011 Sep 29;2011:bar032. Print 2011. PubMed PMID: 21959865.
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150 P2CS - Prokaryotic 2-Component Systems
http://www.p2cs.org		 Database of prokaryotic two-component system signal transduction proteins.
Chen YF, Shin SJ, Lin SR. Ets1 was significantly activated by ERK1/2 in mutant K-ras stably transfected human adrenocortical cells. DNA Cell Biol. 2005 Feb;24(2):126-32. PubMed PMID: 15699632.
2009
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151 PathArt - Pathway Articulator
http://www.jubilantbiosys.com/pathart.html		 Comprehensive collection of curated data from literature for signaling and metabolic pathways. Displays pathways in a dynamic way and includes modules to analyze the microarray data.
Chen YF, Shin SJ, Lin SR. Ets1 was significantly activated by ERK1/2 in mutant K-ras stably transfected human adrenocortical cells. DNA Cell Biol. 2005 Feb;24(2):126-32. PubMed PMID: 15699632.
2005
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152 PathCase
http://nashua.cwru.edu/pathways		 Pathway database and associated tool to store, compare, query and visualize the pathways.
Krishnamurthy L, Nadeau J, Ozsoyoglu G, Ozsoyoglu M, Schaeffer G, Tasan M, Xu W. Pathways database system: an integrated system for biological pathways. Bioinformatics. 2003 May 22;19(8):930-7. PubMed PMID: 12761054.
2003
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153 PathDB - Pathways Database
http://www.ncgr.org/pathdb		 Finding all the pathways or phenotypes associated with the genes in a cluster or validating computationally predicted association with biological data.
P Mendes. Pathdb: a second generation metabolic database. 9th International BioThermoKinetics Meeting, 2000.
2000
100
URL could not be retrieved (10/01/2012).
154 PathDIP - Pathway Database for Integrated and Predictive Pathway Analysis
https://ophid.utoronto.ca/pathDIP/		 PathDIP is a comprehensive resource that integrates known pathway data from multiple sources and predicts additional pathway interactions using computational methods. It combines manually curated pathways with protein-protein interactions, gene expression data, and other omics datasets to provide a more complete view of molecular pathways.
Rahmati, S., Abovsky, M., Pastrello, C., & Jurisica, I. (2017). pathDIP: an annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis. Nucleic acids research, 45(D1), D419–D426. https://doi.org/10.1093/nar/gkw1082
2017
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155 PathLocdb
http://pathloc.cbi.pku.edu.cn		 Search and comparison of the metabolic pathway by their subcellular localization and organisms. Discover the regulatory mechanisms of these pathways.
Zhao M, Qu H. PathLocdb: a comprehensive database for the subcellular localization of metabolic pathways and its application to multiple localization analysis. BMC Genomics. 2010 Dec 2;11 Suppl 4:S13. PubMed PMID: 21143796; PubMed Central PMCID: PMC3005916.
2010
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156 PathoPlant
http://www.pathoplant.de		 Plant pathogenesis pathways and interactions.
BFClow 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
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157 Pathway Slides & Charts
http://www.sigmaaldrich.com/life-science/cell-biology/learning-center/pathway-slides-and.html		 Pathway diagrams provided in the form of ppts.
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158 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
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159 PMAP - The Proteolysis Map
http://www.proteolysis.org		 Reconstruction, modeling and curation of proteolytic pathways and signaling pathways.
Igarashi Y, Heureux E, Doctor KS, Talwar P, Gramatikova S, Gramatikoff K, Zhang Y, Blinov M, Ibragimova SS, Boyd S, Ratnikov B, Cieplak P, Godzik A, Smith JW, Osterman AL, Eroshkin AM. PMAP: databases for analyzing proteolytic events and pathways. Nucleic Acids Res. 2009 Jan;37(Database issue):D611-8. Epub 2008 Oct 8. PubMed PMID: 18842634; PubMed Central PMCID: PMC2686432.
2009
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160 PRIME - PRotein Interactions and Molecular Information databasE
http://prime.ontology.ims.u-tokyo.ac.jp:8081		 Integrated gene/protein informatics database based on natural language processing.
Koike A, Takagi T. PRIME: automatically extracted PRotein Interactions and Molecular Information databasE. In Silico Biol. 2005;5(1):9-20. PubMed PMID:15972002.
2005
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URL could not be retrieved (10/01/2012).
161 ProcessDB
http://www.integrativebioinformatics.com/processdb.html		 Supports mathematical modelling of pathways.
Chasson, A. K. and R. D. Phair. ProcessDB: A cellular process database supporting large-scale iterative kinetic modeling in cell biology. 2nd International Conference on Systems Biology (ICSB2001), Pasadena, CA, 2001.
2001
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162 Prodonet
http://www.prodonet.tu-bs.de		 Visualization network for regulatory tools.
Klein J, Leupold S, MFCnch R, Pommerenke C, Johl T, KE4rst U, JE4nsch L, Jahn D, Retter I. ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W460-4. Epub 2008 Apr 25. PubMed PMID: 18440972; PubMed Central PMCID:PMC2447764.
2008
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163 Protein Lounge
http://www.proteinlounge.com		 Contains curated pathways for many different organisms.
Besaw M. E. (2013). Protein Lounge. Journal of the Medical Library Association : JMLA, 101(2), 164. https://doi.org/10.3163/1536-5050.101.2.019
2013
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164 PRRDB - Pattern recognition receptor database
http://www.imtech.res.in/raghava/prrdb		 Information on receptor-ligand interaction.
Lata S, Raghava GP. PRRDB: a comprehensive database of pattern-recognition receptors and their ligands. BMC Genomics. 2008 Apr 18;9:180. PubMed PMID:18423032; PubMed Central PMCID: PMC2346480.
2008
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165 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
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166 PUMA2 - Evolutionary Analysis of Metabolism
http://compbio.mcs.anl.gov/puma2		 Produce metabolic reconstruction for sequenced genomes.
Maltsev N, Glass E, Sulakhe D, Rodriguez A, Syed MH, Bompada T, Zhang Y, D'Souza M. PUMA2--grid-based high-throughput analysis of genomes and metabolic pathways. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D369-72. PubMed PMID: 16381888; PubMed Central PMCID: PMC1347457.
2006
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URL could not be retrieved (10/01/2012).
167 PUMAdb - Princeton University MicroArray database
http://puma.princeton.edu		 Stores raw and normalized data from microarray experiments.
Selkov E Jr, Grechkin Y, Mikhailova N, Selkov E. MPW: the Metabolic Pathways Database. Nucleic Acids Res. 1998 Jan 1;26(1):43-5. PubMed PMID: 9407141; PubMed Central PMCID: PMC147231.
1998
100
Registration required to access the resource.
168 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
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169 Rahnuma
http://portal.stats.ox.ac.uk:8080/rahnuma		 A tool for prediction and comparison of metabolic networks. Computes all possible pathways between two metabolites.
Mithani A, Preston GM, Hein J. Rahnuma: hypergraph-based tool for metabolic pathway prediction and network comparison. Bioinformatics. 2009 Jul 15;25(14):1831-2. Epub 2009 Apr 27. PubMed PMID: 19398450.
2009
100
License required to access the resource.
170 RAMEDIS - Rare Metabolic Diseases Database
http://www.ramedis.de		 Information on metabolic diseases.
Mischke U, Scholz U, Toepel T, Scheible D, Hofestaedt R, Trefz F. RAMEDIS-rare metabolic diseases publishing tool for genotype-phenotype correlation. Stud Health Technol Inform. 2001;84(Pt 2):970-4. PubMed PMID: 11604876.
2001
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171 RegAnalyst
http://www.nii.ac.in/~deepak/RegAnalyst		 Tool for analysis of regulatory network that integrates motif prediction program and pattern detection tool.
Sharma D, Mohanty D, Surolia A. RegAnalyst: a web interface for the analysis of regulatory motifs, networks and pathways. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W193-201. Epub 2009 May 21. PubMed PMID: 19465400; PubMed Central PMCID: PMC2703886.
2009
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172 ROSPath - Reactive Oxygen Species related Signaling Pathway
http://rospath.ewha.ac.kr		 Database for proteins involved in ROS signaling pathway.
Paek E, Park J, Lee KJ. Multi-layered representation for cell signaling pathways. Mol Cell Proteomics. 2004 Oct;3(10):1009-22. Epub 2004 Aug 2. PubMed PMID: 15289508.
2004
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173 SABIO-RK - System for the Analysis of Biochemical Pathways-Reaction Kinetics
http://sabiork.h-its.org		 Web-based application that contains information about biochemical reactions and their kinetic equation with their parameters.
Rojas I, Golebiewski M, Kania R, Krebs O, Mir S, Weidemann A, Wittig U. Storing and annotating of kinetic data. In Silico Biol. 2007;7(2 Suppl):S37-44.PubMed PMID: 17822389.
2007
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174 SABiosciences: Pathway Central
http://www.sabiosciences.com/pathwaycentral.php		 A resource for pathway reviews, pathway maps and relevant research products. Built by SABiosciences with corporate partners including Protein Lounge. It provides relevant research products such as PCR arrays, PCR primers. Also allows to download powerpoint slides of pathway maps.
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Registration required to download editable pathway maps.
175 SBML.org - Systems Biology Markup Language
http://sbml.org/Models		 A repository of biological simulations models in the Systems Biology Markup Language.
Gay S, Soliman S, Fages F. A graphical method for reducing and relating models in systems biology. Bioinformatics. 2010 Sep 15;26(18):i575-81. PubMed PMID:20823324; PubMed Central PMCID: PMC2935413.
2010
100
URL could not be retrieved
176 SENTRA
http://compbio.mcs.anl.gov/sentra		 Database of microbial signal transduction.
D'Souza M, Romine MF, Maltsev N. SENTRA, a database of signal transduction proteins. Nucleic Acids Res. 2000 Jan 1;28(1):335-6. PubMed PMID: 10592266; PubMed Central PMCID: PMC102390.
2000
100
URL could not be retrieved (10/01/2012).
177 ShiKimate Pathway DataBase (SKPDB)
http://lsbzix.rc.unesp.br/skpdb/		 The ShiKimate Pathway DataBase is a specialized database focused on the shikimate pathway, which is essential for the biosynthesis of aromatic amino acids and other secondary metabolites in microorganisms and plants. SKPDB compiles detailed information on enzymes, genes, metabolites, reactions, and regulatory mechanisms involved in this pathway.
Arcuri, H. A., Zafalon, G. F., Marucci, E. A., Bonalumi, C. E., da Silveira, N. J., Machado, J. M., de Azevedo, W. F., Jr, & Palma, M. S. (2010). SKPDB: a structural database of shikimate pathway enzymes. BMC bioinformatics, 11, 12. https://doi.org/10.1186/1471-2105-11-12
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178 SigPath
http://icb.med.cornell.edu/services/sp-prod/sigpath		 Prototype database designed to support quantitative studies on the signaling pathways and network of the cell.
Campagne F, Neves S, Chang CW, Skrabanek L, Ram PT, Iyengar R, Weinstein H.Quantitative information management for the biochemical computation of cellular networks. Sci STKE. 2004 Aug 24;2004(248):pl11. PubMed PMID: 15340175.
2004
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179 SPAD - Signaling Pathway Database
http://www.grt.kyushu-u.ac.jp/spad		 Overview of signal transduction pathways, gives details of protein-protein interaction, protein-DNA interaction and the sequence of DNA and proteins.
Tateishi N., Shiotari H., Kuhara S., Takagi T., Kanehisa M. An integrated database SPAD (signaling pathway database) for signal transduction and genetic information. Proceedings of the Genome Informatics Workshop (GIW95); December 11-12. Yokohama, Japan; 1995. p. 160-161.
1995
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180 SPIKE - Signaling Pathway Integrated Knowledge Engine
http://www.cs.tau.ac.il/~spike		 Information on signaling pathways.
Elkon R, Vesterman R, Amit N, Ulitsky I, Zohar I, Weisz M, Mass G, Orlev N,Sternberg G, Blekhman R, Assa J, Shiloh Y, Shamir R. SPIKE--a database, visualization and analysis tool of cellular signaling pathways. BMC Bioinformatics. 2008 Feb 20;9:110. PubMed PMID: 18289391; PubMed Central PMCID: PMC2263022.
2008
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181 STCDB - Signal Transduction Classification Database
http://bibiserv.techfak.uni-bielefeld.de/stcdb		 Contains general information on signal transduction classification.
Chen M, Lin S, Hofestaedt R. STCDB: Signal Transduction Classification Database. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D456-8. PubMed PMID: 14681456; PubMed Central PMCID: PMC308813.
2004
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182 STKE - Signal Transduction Knowledge Environment
http://stke.sciencemag.org		 Curated resource of signal transduction information.
Gough NR. Science's signal transduction knowledge environment: the connections maps database. Ann N Y Acad Sci. 2002 Oct;971:585-7. PubMed PMID: 12438188.
2002
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183 SYSTOMONAS - SYSTems biology of pseudOMONAS
http://systomonas.tu-bs.de		 Provides broad range of information on the genes, proteins, metabolome experiment results as well as regulatory network.
Choi C, MFCnch R, Leupold S, Klein J, Siegel I, Thielen B, Benkert B, Kucklick M, Schobert M, Barthelmes J, Ebeling C, Haddad I, Scheer M, Grote A, Hiller K,Bunk B, Schreiber K, Retter I, Schomburg D, Jahn D. SYSTOMONAS--an integrated database for systems biology analysis of Pseudomonas. Nucleic Acids Res. 2007 Jan;35(Database issue):D533-7. PubMed PMID: 17202169; PubMed Central PMCID:PMC1899106.
2007
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184 TORQUE - Topology-Free Querying of Protein Interaction Networks
http://www.cs.tau.ac.il/~bnet/torque.html		 Information regarding protein interaction networks.
Bruckner S, HFCffner 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.
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Installation required.
185 TRMP - Therapeutically Relevant Multiple Pathways Database
http://bidd.nus.edu.sg/group/trmp/trmp_ns.asp		 Database of disease relevant pathways with annotated drug targets and links to drugs.
Zheng CJ, Zhou H, Xie B, Han LY, Yap CW, Chen YZ. TRMP: a database of therapeutically relevant multiple pathways. Bioinformatics. 2004 Sep 22;20(14):2236-41. Epub 2004 Apr 1. PubMed PMID: 15059817.
2004
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186 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
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187 UM-BBD - University of Minnesota Biocatalysis/Biodegradation Database
http://umbbd.msi.umn.edu		 Exclusively showcases the biocatalysis and biodegradation pathways, pathway prediction system.
Ellis LB, Speedie SM, McLeish R. Representing metabolic pathway information: an object-oriented approach. Bioinformatics. 1998;14(9):803-6. PubMed PMID:9918950.
1998
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188 VISIBIOweb
http://visibioweb.patika.org		 Web based pathway visualization.
Dilek A, Belviranli ME, Dogrusoz U. VISIBIOweb: visualization and layout services for BioPAX pathway models. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W150-4. Epub 2010 May 11. PubMed PMID: 20460470; PubMed Central PMCID:PMC2896092.
2010
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189 VitaPad
http://bioinformatics.med.yale.edu		 Enables users to create and modify biological pathway diagrams.
Holford M, Li N, Nadkarni P, Zhao H. VitaPad: visualization tools for the analysis of pathway data. Bioinformatics. 2005 Apr 15;21(8):1596-602. Epub 2004 Nov 25. PubMed PMID: 15564306.
2004
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190 Wnt Database
http://www.stanford.edu/group/nusselab/cgi-bin/wnt		 Information on Wnt signaling pathway and proteins involved, mutation in the pathway or in the genes, etc.
Not available
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191 XPD - Phosphorylation Site Database
http://vigen.biochem.vt.edu/xpd/xpd.htm		 Database of protein phosphorylation sites.
Wurgler-Murphy SM, King DM, Kennelly PJ. The Phosphorylation Site Database: A guide to the serine-, threonine-, and/or tyrosine-phosphorylated proteins in prokaryotic organisms. Proteomics. 2004 Jun;4(6):1562-70. PubMed PMID: 15174126.
2004
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URL: temporarily unavailable (10/01/2012).
192 XtalkDB - Crosstalk Database
http://www.xtalkdb.org/home		 XtalkDB is a specialized resource that provides curated information on molecular crosstalk between different cellular signaling pathways. It integrates data from multiple sources to map interactions between pathways, helping researchers understand how signaling networks influence each other in various biological processes and diseases.
Sam, S. A., Teel, J., Tegge, A. N., Bharadwaj, A., & Murali, T. M. (2017). XTalkDB: a database of signaling pathway crosstalk. Nucleic acids research, 45(D1), D432–D439. https://doi.org/10.1093/nar/gkw1037
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