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A comparative account of pathways, feature-validations and application-based categorizations : Pathways in humans
S.NoResources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
1 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.
Not available
Not available
1
2 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
100
3 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
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4 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
5 BioModels database
http://www.ebi.ac.uk/biomodels-main
Provides published, per-reviewed, quantitative models of biochemical and cellular systems.
Le Nov\E8re 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
100
6 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
7 Cancer Cell Map
http://cancer.cellmap.org/cellmap/
Selected set of human cancer focused pathways.
Not available
Not available
100
8 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.
License required to access the resource.
9 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
10 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
100
11 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
12 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
100
 Registration required to access the resource.
Registration required to access the resource.
13 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).
URL could not be retrieved (10/01/2012).
14 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
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15 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
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 Requires JAVA +5.0.
Requires JAVA +5.0.
16 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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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
100
 Registration required to access the resource.
Registration required to access the resource.
18 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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19 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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20 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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21 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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22 HMDB - Human Metabolome Database
http://www.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
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23 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.
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24 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
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25 InnateDB - A Knowledge Resource for Innate Immunity Interactions and Pathways
http://www.innatedb.ca
Text mining, pathway diagram tools, interaction or functional association prediction.
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.
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26 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.
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
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27 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
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28 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
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29 MACPAK - Simulatable Macrophage Pathway Knowledgebase
http://macpak.csml.org
Focused on LPS-induced macrophage signaling pathways, contains pathways for genes derived from many reports.
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.
2011
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30 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
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 License required to access the resource.
License required to access the resource.
31 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
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32 METAPATH
http://scopes.biologie.hu-berlin.de/index.php?m=path
Calculation of minimal synthesis pathway.
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.
2007
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33 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
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34 Millipore Pathways
http://www.millipore.com/pathways/pw/pathways
Browse for pathways with respect to disease areas.
Not available
Not available
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35 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
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36 MODOMICS
http://genesilico.pl/modomics
Database of RNA modification pathways.
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.
2006
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37 Molecule Pages
http://www.signaling-gateway.org
Cell signaling database designed to facilitate navigation of complex world of research.
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.
2002
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38 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
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39 NetPath
http://www.netpath.org
A curated resource of signal transduction pathways.
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.
2009
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40 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.
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.
2011
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41 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
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42 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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43 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
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44 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
100
 Requires JAVA +5.0.
Requires JAVA +5.0.
45 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
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46 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
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47 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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48 Protein Lounge
http://www.proteinlounge.com
Contains curated pathways for many different organisms.
Not available
Not available
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49 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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50 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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51 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
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52 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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53 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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54 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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55 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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56 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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57 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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58 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.
Not available
Not available
100
 Registration required to download editable pathway maps.
Registration required to download editable pathway maps.
59 SignaLink
http://signalink.org
Allows system level analysis using the network of intracellular signaling pathways.
Korcsm\E1ros 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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60 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
100
61 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
100
62 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
100
63 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
100
64 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.
2010
100
 Installation required.
Installation required.
65 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
100
66 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
67 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
68 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
69 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
Not available
100
 
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