| 1 |
BioCychttp://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 |
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| 2 |
CPA - Comparative Pathway Analyzerhttp://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 |
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| 3 |
FMM - From Metabolite to Metabolitehttp://FMM.mbc.nctu.edu.tw |
| Reconstruct the pathway from one metabolite to another, comparison of the pathway among species. |
| | Chou CH, Chang WC, Chiu CM, Huang CC, Huang HD. FMM: a web server for metabolic pathway reconstruction and comparative analysis. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W129-34. Epub 2009 Apr 28. PubMed PMID: 19401437; PubMed Central PMCID: PMC2703958. |
| 2009 | 100 |
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| 4 |
GeneMANIA http://www.genemania.org |
| Finds other genes related to a set of input genes, using a very large set of functional association data. |
| | Mostafavi S, Ray D, Warde-Farley D, Grouios C, Morris Q. GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function. Genome Biol. 2008;9 Suppl 1:S4. Epub 2008 Jun 27. PubMed PMID: 18613948; PubMed Central PMCID: PMC2447538. |
| 2008 | 100 |
Requires JAVA +5.0.
Requires JAVA +5.0. |
| 5 |
JWS - Java Web Simulationhttp://jjj.biochem.sun.ac.za |
| Repository of kinetic models describing biological systems which can be interactively run and interrogated over the internet. |
| | Snoep JL, Olivier BG. Java Web Simulation (JWS); a web based database of kinetic models. Mol Biol Rep. 2002;29(1-2):259-63. PubMed PMID: 12241068. |
| 2002 | 100 |
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| 6 |
KEGG - Kyoto Encyclopedia of Genes and Genomeshttp://www.genome.jp/kegg |
| Database of metabolic pathways from different organisms, also provides reference pathways that describe a general pathway which is then projected onto a genome based on the presence of pathway enzymes in that genome. |
| | Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 1999 Jan 1;27(1):29-34.PubMed PMID: 9847135; PubMed Central PMCID: PMC148090. |
| 1999 | 100 |
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| 7 |
MetaCyc - Metabolic Pathway Databasehttp://metacyc.org |
| Contains pathways from different organisms. |
| | Krieger CJ, Zhang P, Mueller LA, Wang A, Paley S, Arnaud M, Pick J, Rhee SY, Karp PD. MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D438-42. PubMed PMID: 14681452; PubMed Central PMCID: PMC308834. |
| 2004 | 100 |
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| 8 |
METAPATHhttp://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 | 100 |
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| 9 |
MetExplorehttp://metexplore.toulouse.inra.fr/metexploreJoomla/index.php |
| A web resource that offers the possibility to link the metabolites identified in untargetted metabolomics experiments within the context of genome scale reconstructed metabolic network. |
| | Cottret L, Wildridge D, Vinson F, Barrett MP, Charles H, Sagot MF, Jourdan F. MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W132-7. Epub 2010 May 5. PubMed PMID: 20444866; PubMed Central PMCID: PMC2896158. |
| 2010 | 100 |
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| 10 |
MiMI - Michigan Molecular Interactionshttp://mimi.ncibi.org/MimiWeb/main-page.jsp |
| Contains pathway diagrams from KEGG and Reactome. |
| | Jayapandian M, Chapman A, Tarcea VG, Yu C, Elkiss A, Ianni A, Liu B, Nandi A, Santos C, Andrews P, Athey B, States D, Jagadish HV. Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. Nucleic Acids Res. 2007 Jan;35(Database issue):D566-71. Epub 2006 Nov 27. PubMed PMID: 17130145; PubMed Central PMCID: PMC1716720. |
| 2006 | 100 |
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| 11 |
NCBI BioSystemshttp://www.ncbi.nlm.nih.gov/biosystems |
| Connects biosystem records with the associated literature, molecular and chemical data. |
| | Evsikov AV, Dolan ME, Genrich MP, Patek E, Bult CJ. MouseCyc: a curated biochemical pathways database for the laboratory mouse. Genome Biol. 2009;10(8):R84. Epub 2009 Aug 14. PubMed PMID: 19682380; PubMed Central PMCID:PMC2745765. |
| 2009 | 100 |
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| 12 |
PANTHER - Protein ANalysis Through Evolutionary Relationshipshttp://www.pantherdb.org |
| Gene expression data analysis, comparison of gene lists. |
| | Mi H, Lazareva-Ulitsky B, Loo R, Kejariwal A, Vandergriff J, Rabkin S, Guo N, Muruganujan A, Doremieux O, Campbell MJ, Kitano H, Thomas PD. The PANTHERdatabase of protein families, subfamilies, functions and pathways. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D284-8. PubMed PMID: 15608197; PubMed Central PMCID: PMC540032. |
| 2005 | 100 |
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| 13 |
Pathway Commonshttp://www.pathwaycommons.org/pc/ |
| Provides researchers with convenient access to the collection of publicly available pathways from many different organisms. |
| | Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, Schultz N, Bader GD, Sander C. Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res. 2011 Jan;39(Database issue):D685-90. Epub 2010 Nov 10. PubMed PMID: 21071392; PubMed Central PMCID: PMC3013659. |
| 2010 | 100 |
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| 14 |
Protein Loungehttp://www.proteinlounge.com |
| Contains curated pathways for many different organisms. |
| | Not available | 100 |
|
| 15 |
pSTIING - Protein, Signalling, Transcriptional Interactions & Inflammation Networks Gatewayhttp://pstiing.licr.org |
| Intergrated database of molecular association and transcriptional regulatory networks. |
| | Ng A, Bursteinas B, Gao Q, Mollison E, Zvelebil M. pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D527-34. PubMed PMID: 16381926; PubMed Central PMCID: PMC1347407. |
| 2006 | 100 |
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| 16 |
R spiderhttp://mips.helmholtz-muenchen.de/proj/rspider |
| Analysis of the list of genes, exploiting the KEGG and Reactome Knowledgebases. |
| | Antonov AV, Schmidt EE, Dietmann S, Krestyaninova M, Hermjakob H. R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W78-83. Epub 2010 Jun 2. PubMed PMID: 20519200; PubMed Central PMCID: PMC2896180. |
| 2010 | 100 |
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| 17 |
SignaLinkhttp://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 | 100 |
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| 18 |
TORQUE - Topology-Free Querying of Protein Interaction Networkshttp://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. |
| 19 |
TRRD - Transcription Regulatory Regions Databasehttp://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 |
|
| 20 |
VisANThttp://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 |
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| 21 |
WikiPathwayshttp://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 |
|
| 22 |
Wnt Databasehttp://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 | 100 |
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