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Molecular Pathway Diagrams

Individual Diagram Pages

These can be accessed directly from the list that catalogs them alphabetically based on the major nodes of the pathway ontology. Alternatively, one can search the pathway ontology for terms of interest; the ontology report page provides an icon with a link to the diagram page if one exists for that term. Click here to view choices of molecular pathways.

Molecular Pathway Suites and Suite Networks

The suites and suite networks offer an instant snapshot of pathways that are connected within a larger context or suites inter-related within a higher order network. The alphabetically listed suites and suite networks can be accessed here.

Pathway-related Publications by RGD Members

Disease, models, variants and altered pathways – journeying RGD through the magnifying glass.
Petri V, Hayman GT, Tutaj M, Smith JR, Laulederkind SJ, Wang SJ, Nigam R, De Pons J, Shimoyama M, Dwinell MR. Comput Struct Biotechnol J. 2015 Nov; 14:35-48.

Disease pathways at the Rat Genome Database Pathway Portal: genes in context – a network approach to understanding the molecular mechanisms of disease.
Petri V, Hayman GT, Tutaj M, Smith JR, Laulederkind SJF, Wang S-J, Nigam R, De Pons J, Shimoyama M, Dwinell MR, Worthey EA, Jacob HJ. Hum Genomics. 2014 Sep; 8(1):17.

The pathway ontology – updates and applications.
Petri V, Jayaraman P, Tutaj M, Hayman GT, Smith JR, De Pons J, Laulederkind SJ, Lowry TF, Nigam R, Wang SJ, Shimoyama M, Dwinell MR, Munzenmaier DH, Worthey EA, Jacob HJ. J Biomed Semantics. 2014 Feb; 5(1):7.

The updated RGD Pathway Portal utilizes increased curation efficiency and provides expanded pathway information.
Hayman GT, Jayaraman P, Petri V, Tutaj M, Liu W, De Pons J, Dwinell MR, Shimoyama M, Worthey E, Munzenmaier DH, Jacob HJ. Hum Genomics. 2013 Feb; 7(1):4.

Pathway Resources at the Rat Genome Database: A Dynamic Platform for Integrating Gene, Pathway and Disease Information.
Petri, V. Chapter 14 in Handbook of Research on Computational and Systems Biology: Interdisciplinary Applications, IGI Global Publishers, 2011.

The rat genome database pathway portal.
Petri V, Shimoyama M, Hayman GT, Smith JR, Tutaj M, de Pons J, Dwinell MR, Munzenmaier DH, Twigger SN, Jacob HJ; RGD Team. Database (Oxford). 2011 Apr 8;2011:bar010. Print 2011.
PMID: 21478484

The BioPAX community standard for pathway data sharing.
Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D’Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Reubenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Le Novère N, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD. Nat Biotechnol. 2010 Sep; 28(9): 935-42. Epub 2010 Sep 9.
PMID: 20829833
Corrigendum: Nat Biotechnol. 2012 Apr;30(4):365. Reubenacker O [corrected to Ruebenacker O].

The Rat Genome Database 2009: variation, ontologies and pathways.
Dwinell MR, Worthey EA, Shimoyama M, Bakir-Gungor B, DePons J, Laulederkind S, Lowry T, Nigam R, Petri V, Smith J, Stoddard A, Twigger SN, Jacob HJ; RGD Team. Nucleic Acids Res. 2009 Jan; 37(Database issue): D744-9. Epub 2008 Nov 7.
PMID: 18996890

Pathway-related Information and Data Links

RGD Pathway Portal Overview RGD’s Pathway Ontology OBO file The Pathway Ontology at NCBO’s BioPortal
Rat Gene-to-Pathway Annotations File Human Gene-to-Pathway Annotations File Mouse Gene-to-Pathway Annotations File



RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.