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Lab. Bio-Trac 40 (Protein Bioinformatics) October 9, 2008 Zhang-Zhi Hu, M.D. Research Associate Professor Protein Information Resource, Department of Biochemistry and Molecular & Cellular Biology Georgetown University Medical Center. http://www.geneontology.org/.

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  1. Lab Bio-Trac 40 (Protein Bioinformatics) October 9, 2008 Zhang-Zhi Hu, M.D. Research Associate Professor Protein Information Resource, Department of Biochemistry and Molecular & Cellular Biology Georgetown University Medical Center

  2. http://www.geneontology.org/

  3. GO search and display tool Leaf node GO term (GO:0006366): mRNA transcription from RNA polymerase II promoter

  4. Human p53 – GO annotation (UniProtKB:P04637) GO:0006289:nucleotide-excision repair [PMID:7663514; evidence:IMP] http://pir.georgetown.edu/cgi-bin/ipcEntry?id=P04637

  5. ~46 Human, mouse, plant, worm, yeast … GO annotation of gene products • Science basis of the GO: trained experts use the experimental observations from literature to associate GO terms with gene products (to annotate the entities represented in the gene/protein databases) • Enabling data integration across databases and making them available to semantic search http://www.geneontology.org/GO.current.annotations.shtml

  6. Functional profiling ID Mapping Batch gene/protein retrieval and profiling Enter ID, gi # Information matrix http://pir.georgetown.edu/pirwww/search/idmapping.shtml

  7. Entrez Gene list 5717 4917 8507 117157 9723 5198 4114 7746 26227 4440 10328 9875 4976 1826 1500 9683 8541 23464 9247 23020 UniProt Accession/ID Batch retrieval http://pir.georgetown.edu/pirwww/search/batch.shtml http://pir.georgetown.edu/cgi-bin/batch_iprox.pl?search=1&data=gu1 http://pir.georgetown.edu/pirwww/search/idmapping.shtml

  8. GO Slim http://www.geneontology.org/GO.slims.shtml (http://www.geneontology.org/)

  9. KEGG Metabolic & Regulatory Pathways • KEGG is a suite of databases and associated software, integrating our current knowledge on molecular interaction networks, the information of genes and proteins, and of chemical compounds and reactions. (http://www.genome.ad.jp/kegg/pathway.html) Transforming Growth Factor (TGF) beta signaling

  10. BioCarta Cellular Pathways (http://www.biocarta.com/index.asp) Transforming Growth Factor (TGF) beta signaling [Homo sapiens]

  11. Transforming Growth Factor (TGF) beta signaling [Homo sapiens] (http://reactome.org/cgi-bin/eventbrowser?DB=gk_current&FOCUS_SPECIES=Homo%20sapiens&ID=170834&) Reactome: events and objects (including modified forms and complex) Event ->REACT_6879.1: Activated type I receptor phosphorylates R-SMAD directly [Homo sapiens] Object -> REACT_7364.1: Phospho-R-SMAD [cytosol] Event -> REACT_6760.1: Phospho-R-SMAD forms a complex with CO-SMAD [Homo sapiens] Object -> REACT_7344.1: Phospho-R-SMAD:CO-SMAD complex [cytosol] Event -> REACT_6726.1: The phospho-R-SMAD:CO-SMAD transfers to the nucleus Object -> REACT_7382.2: Phospho-R-SMAD:CO-SMAD complex [nucleoplasm] ……

  12. PID Transforming Growth Factor beta signaling

  13. Transforming Growth Factor (TGF) beta signaling PID Reactome ~26 proteins in PID are not defined in Reactome, while only 2 in Reactome not defined in PID

  14. iProXpress: Integrative analysis of proteomic and gene expression data Data MS spectrum Peptide ident. Protein ident. http://pir.georgetown.edu/iproxpress/ Information Function Pathway Family Categorize Statistics Association Knowledge

  15. Organelle proteome data sets iProXpress– Pathway Profiling ER Mit • Protein information matrix: extensive annotations including protein name, family classification, function, protein-protein interaction, pathway… • Functional profiling: iterative categorization, sorting, cross-dataset comparison, coupled with manual examination. Mit ER KEGG pathway

  16. DNA synthesis DNA repair dGTP X GTP dGDPGDP ATP X dATP ADPdADP Ribonucleoside diphosphate reductase subunit M2 (RRM2) 1.17.4.1 1.17.4.1 Purine metabolic pathway

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