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Total resources - 12
A comparative account of pathways, feature-validations and application-based categorizations : Pathways related to cancer
S.NoResources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
1 BBID - Biological Biochemical Image Database
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.
2 BiologicalNetworks
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.
3 Cancer Cell Map
Selected set of human cancer focused pathways.
Not available
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4 iPAVS - Integrated Pathway Resources, Analysis and Visualization System
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.
5 NetPath
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.
6 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.
7 PathArt - Pathway Articulator
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.
8 Pathway Miner - Classify and Extract Network of Associated Genes/Proteins based on Pathways
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.
Requires JAVA +5.0.
Requires JAVA +5.0.
9 PharmGKB
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.
10 RGD - Rat Genome Database
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.
11 SABiosciences: Pathway Central
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
Registration required to download editable pathway maps.
Registration required to download editable pathway maps.
12 Wnt Database
Information on Wnt signaling pathway and proteins involved, mutation in the pathway or in the genes, etc.
Not available
Not available
copyright © Dr. Kshitish Acharya K; all rights reserved

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