1 |
Pathway Slides & Chartshttp://www.sigmaaldrich.com/life-science/cell-biology/learning-center/pathway-slides-and.html |
Pathway diagrams provided in the form of ppts. |
| | Not available | 1 |
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2 |
BBID - Biological Biochemical Image Databasehttp://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 |
BioCartahttp://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 | 100 |
|
4 |
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 |
|
5 |
BioModels databasehttp://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 Pathwayshttp://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 Maphttp://cancer.cellmap.org/cellmap/ |
Selected set of human cancer focused pathways. |
| | Not available | 100 |
|
8 |
CellCircuitshttp://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 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 |
|
10 |
CPDB - ConsensusPathDBhttp://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.orghttp://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 Networkhttp://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 Databasehttp://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 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 |
|
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 | 100 |
Requires JAVA +5.0. Requires JAVA +5.0. |
16 |
GeneNet - Gene Networkshttp://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 | 100 |
|
17 |
GenMAPP - Gene MicroArray Pathway Profilerhttp://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 Disordershttps://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 | 100 |
|
19 |
GON - Genomic Object Nethttp://genome.ib.sci.yamaguchi-u.ac.jp/~gon/index |
Software platform for biological pathway modeling and simulation. |
| Matsuno H, Doi A, Nagasaki M, Miyano S. Hybrid Petri net representation of gene regulatory network. Pac Symp Biocomput. 2000:341-52. PubMed PMID: 10902182. |
| 2000 | 100 |
|
20 |
HCPIN - Human Cancer Protein Interaction Networkhttp://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 | 100 |
|
21 |
hiPathDB - human-integrated pathway databasehttp://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 | 100 |
|
22 |
HMDB - Human Metabolome Databasehttp://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 | 100 |
|
23 |
HPD - Human Pathway Databasehttp://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 | 100 |
|
24 |
HumanCychttp://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 | 100 |
|
25 |
InnateDB - A Knowledge Resource for Innate Immunity Interactions and Pathwayshttp://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. |
| 2008 | 100 |
|
26 |
iPAVS - Integrated Pathway Resources, Analysis and Visualization Systemhttp://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 | 100 |
|
27 |
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 |
|
28 |
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 |
|
29 |
MACPAK - Simulatable Macrophage Pathway Knowledgebasehttp://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 | 100 |
|
30 |
MetaCorehttp://www.genego.com/metacore.php |
Database of molecular cellular pathways, and is designed to integrate data from different levels of cellular function. |
| Ekins S, Nikolsky Y, Bugrim A, Kirillov E, Nikolskaya T. Pathway mapping tools for analysis of high content data. Methods Mol Biol. 2007;356:319-50. Review. PubMed PMID: 16988414. |
| 2007 | 100 |
License required to access the resource. License required to access the resource. |
31 |
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 |
|
32 |
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 |
|
33 |
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 |
|
34 |
Millipore Pathwayshttp://www.millipore.com/pathways/pw/pathways |
Browse for pathways with respect to disease areas. |
| | Not available | 100 |
|
35 |
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 |
|
36 |
MODOMICShttp://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 | 100 |
|
37 |
Molecule Pageshttp://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 | 100 |
|
38 |
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 |
|
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 | 100 |
|
40 |
NetSlimhttp://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 | 100 |
|
41 |
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 |
|
42 |
PathArt - Pathway Articulatorhttp://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 | 100 |
|
43 |
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 |
|
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 |
PharmGKBhttp://www.pharmgkb.org |
| 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 | 100 |
|
46 |
PID - NCI-Nature Pathway Interaction Databasehttp://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 | 100 |
|
47 |
PMAP - The Proteolysis Maphttp://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 | 100 |
|
48 |
Protein Loungehttp://www.proteinlounge.com |
Contains curated pathways for many different organisms. |
| | Not available | 100 |
|
49 |
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 |
|
50 |
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 |
|
51 |
Reactomehttp://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 | 100 |
|
52 |
RegPhoshttp://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 | 100 |
|
53 |
REPAIRtoire - A database of DNA repair pathwayshttp://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 | 100 |
|
54 |
ResponseNethttp://bioinfo.bgu.ac.il/respnet |
Reveals signaling and regulatory networks linking genetic and transcriptomic screening data. |
| Lan A, Smoly IY, Rapaport G, Lindquist S, Fraenkel E, Yeger-Lotem E.ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W424-9. Epub 2011 May 16. PubMed PMID: 21576238; PubMed Central PMCID:PMC3125767. |
| 2011 | 100 |
|
55 |
RGD - Rat Genome Databasehttp://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 | 100 |
|
56 |
ROSPath - Reactive Oxygen Species related Signaling Pathwayhttp://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 | 100 |
|
57 |
SABIO-RK - System for the Analysis of Biochemical Pathways-Reaction Kineticshttp://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 | 100 |
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58 |
SABiosciences: Pathway Centralhttp://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 | 100 |
Registration required to download editable pathway maps. Registration required to download editable pathway maps. |
59 |
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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60 |
SMPDB - Small Molecule Pathway Databasehttp://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 |
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61 |
SPIKE - Signaling Pathway Integrated Knowledge Enginehttp://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 |
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62 |
STCDB - Signal Transduction Classification Databasehttp://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 |
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63 |
T1DBasehttp://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 |
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64 |
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. |
65 |
TRMP - Therapeutically Relevant Multiple Pathways Databasehttp://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 |
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66 |
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 |
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67 |
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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68 |
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 |
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69 |
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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