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Total resources - 15
A comparative account of pathways, feature-validations and application-based categorizations : Pathways for a specific disease
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
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
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
100
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
100
KEGG - Kyoto Encyclopedia of Genes and Genomes
http://www.genome.jp/kegg
Database of metabolic pathways from different organisms, also provides reference pathways that describe a general pathway which is then projected onto a genome based on the presence of pathway enzymes in that genome.
Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 1999 Jan 1;27(1):29-34.PubMed PMID: 9847135; PubMed Central PMCID: PMC148090.
1999
100
MetaCore
http://www.genego.com/metacore.php
Database of molecular cellular pathways, and is designed to integrate data from different levels of cellular function.
Ekins S, Nikolsky Y, Bugrim A, Kirillov E, Nikolskaya T. Pathway mapping tools for analysis of high content data. Methods Mol Biol. 2007;356:319-50. Review. PubMed PMID: 16988414.
2007
100
License required to access the resource.
Millipore Pathways
http://www.millipore.com/pathways/pw/pathways
Browse for pathways with respect to disease areas.
Not available
Not available
100
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
100
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.
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
100
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
100
Protein Lounge
http://www.proteinlounge.com
Contains curated pathways for many different organisms.
Not available
Not available
100
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
100
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
100
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
100
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.
 
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