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Literature DB >> 21505029

Signaling gateway molecule pages--a data model perspective.

Ashok Reddy Dinasarapu¹, Brian Saunders, Iley Ozerlat, Kenan Azam, Shankar Subramaniam.

Abstract

SUMMARY: The Signaling Gateway Molecule Pages (SGMP) database provides highly structured data on proteins which exist in different functional states participating in signal transduction pathways. A molecule page starts with astate of a native protein, without any modification and/or interactions. New states are formed with every post-translational modification or interaction with one or more proteins, small molecules or class molecules and with each change in cellular location. State transitions are caused by a combination of one or more modifications, interactions and translocations which then might be associated with one or more biological processes. In a characterized biological state, a molecule can function as one of several entities or their combinations, including channel, receptor, enzyme, transcription factor and transporter. We have also exported SGMP data to the Biological Pathway Exchange (BioPAX) and Systems Biology Markup Language (SBML) as well as in our custom XML. AVAILABILITY: SGMP is available at www.signaling-gateway.org/molecule.

Entities: Chemical

Mesh：

Substances：

Year: 2011 PMID： 21505029 PMCID： PMC3106186 DOI： 10.1093/bioinformatics/btr190

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

10 in total

1. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

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Journal: Nat Genet Date: 2000-05 Impact factor: 38.330

2. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

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Journal: Bioinformatics Date: 2003-03-01 Impact factor: 6.937

3. The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks.

Authors: Sudhir Sivakumaran; Sridhar Hariharaputran; Jyoti Mishra; Upinder S Bhalla
Journal: Bioinformatics Date: 2003-02-12 Impact factor: 6.937

4. The Molecule Pages database.

Authors: Joshua Li; Yuhong Ning; Warren Hedley; Brian Saunders; Yongsheng Chen; Nicole Tindill; Timo Hannay; Shankar Subramaniam
Journal: Nature Date: 2002-12-12 Impact factor: 49.962

Review 5. The KEGG database.

Authors: Minoru Kanehisa
Journal: Novartis Found Symp Date: 2002

6. Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Authors: Paul Shannon; Andrew Markiel; Owen Ozier; Nitin S Baliga; Jonathan T Wang; Daniel Ramage; Nada Amin; Benno Schwikowski; Trey Ideker
Journal: Genome Res Date: 2003-11 Impact factor: 9.043

Review 7. Cell growth control by G protein-coupled receptors: from signal transduction to signal integration.

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Journal: Oncogene Date: 1998-09-17 Impact factor: 9.867

8. The BioPAX community standard for pathway data sharing.

Authors: Emek Demir; Michael P Cary; Suzanne Paley; Ken Fukuda; Christian Lemer; Imre Vastrik; Guanming Wu; Peter D'Eustachio; Carl Schaefer; Joanne Luciano; Frank Schacherer; Irma Martinez-Flores; Zhenjun Hu; Veronica Jimenez-Jacinto; Geeta Joshi-Tope; Kumaran Kandasamy; Alejandra C Lopez-Fuentes; Huaiyu Mi; Elgar Pichler; Igor Rodchenkov; Andrea Splendiani; Sasha Tkachev; Jeremy Zucker; Gopal Gopinath; Harsha Rajasimha; Ranjani Ramakrishnan; Imran Shah; Mustafa Syed; Nadia Anwar; Ozgün Babur; Michael Blinov; Erik Brauner; Dan Corwin; Sylva Donaldson; Frank Gibbons; Robert Goldberg; Peter Hornbeck; Augustin Luna; Peter Murray-Rust; Eric Neumann; Oliver Ruebenacker; Oliver Reubenacker; Matthias Samwald; Martijn van Iersel; Sarala Wimalaratne; Keith Allen; Burk Braun; Michelle Whirl-Carrillo; Kei-Hoi Cheung; Kam Dahlquist; Andrew Finney; Marc Gillespie; Elizabeth Glass; Li Gong; Robin Haw; Michael Honig; Olivier Hubaut; David Kane; Shiva Krupa; Martina Kutmon; Julie Leonard; Debbie Marks; David Merberg; Victoria Petri; Alex Pico; Dean Ravenscroft; Liya Ren; Nigam Shah; Margot Sunshine; Rebecca Tang; Ryan Whaley; Stan Letovksy; Kenneth H Buetow; Andrey Rzhetsky; Vincent Schachter; Bruno S Sobral; Ugur Dogrusoz; Shannon McWeeney; Mirit Aladjem; Ewan Birney; Julio Collado-Vides; Susumu Goto; Michael Hucka; Nicolas Le Novère; Natalia Maltsev; Akhilesh Pandey; Paul Thomas; Edgar Wingender; Peter D Karp; Chris Sander; Gary D Bader
Journal: Nat Biotechnol Date: 2010-09-09 Impact factor: 54.908

9. Reactome: a knowledgebase of biological pathways.

Authors: G Joshi-Tope; M Gillespie; I Vastrik; P D'Eustachio; E Schmidt; B de Bono; B Jassal; G R Gopinath; G R Wu; L Matthews; S Lewis; E Birney; L Stein
Journal: Nucleic Acids Res Date: 2005-01-01 Impact factor: 16.971

10. MouseCyc: a curated biochemical pathways database for the laboratory mouse.

Authors: Alexei V Evsikov; Mary E Dolan; Michael P Genrich; Emily Patek; Carol J Bult
Journal: Genome Biol Date: 2009-08-14 Impact factor: 13.583

10 in total

7 in total

7. Simultaneous Quantification of Serum Nonesterified and Esterified Fatty Acids as Potential Biomarkers to Differentiate Benign Lung Diseases from Lung Cancer.

Authors: Junling Ren; Dan Zhang; Yujie Liu; Ruiqing Zhang; Huiling Fang; Shuai Guo; Dan Zhou; Mo Zhang; Yupin Xu; Ling Qiu; Zhili Li
Journal: Sci Rep Date: 2016-09-30 Impact factor: 4.379

7 in total

Signaling gateway molecule pages--a data model perspective.

1. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

2. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

3. The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks.

4. The Molecule Pages database.

Review 5. The KEGG database.

6. Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Review 7. Cell growth control by G protein-coupled receptors: from signal transduction to signal integration.

8. The BioPAX community standard for pathway data sharing.

9. Reactome: a knowledgebase of biological pathways.

10. MouseCyc: a curated biochemical pathways database for the laboratory mouse.

Review 1. Bioinformatics and systems biology of the lipidome.

2. Graphene and graphene oxide as a solid matrix for extraction of membrane and membrane-associated proteins.

Review 3. Lipid integration in neurodegeneration: an overview of Alzheimer's disease.

Review 4. Data management strategies for multinational large-scale systems biology projects.

5. B-cell ligand processing pathways detected by large-scale comparative analysis.

Review 6. Physical forces modulate cell differentiation and proliferation processes.

7. Simultaneous Quantification of Serum Nonesterified and Esterified Fatty Acids as Potential Biomarkers to Differentiate Benign Lung Diseases from Lung Cancer.