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Protein Bioinformatics: Functional Profiling and Pathway Analysis

Explore protein information, gene annotations, and molecular pathways for advanced research. Access extensive data integration tools for thorough functional profiling and category analysis. Dive into DNA repair pathways, KEGG networks, and iProXpress insights.

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Protein Bioinformatics: Functional Profiling and Pathway Analysis

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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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