Systems biology at the molecular level is concerned with networks of interacting molecules, their structure, and dynamic response to perturbations that give rise to systems' properties that determine measurable, macroscopic phenotypes. At any time, in any cell, multiple types of molecular networks are concurrently active. One of the most important known regulatory systems in eukaryotic cells is reversible protein phosphorylation catalyzed by protein kinases and phosphatases, respectively. Therefore, it is essential to understand and eventually model the protein phosphorylation-mediated informational fluxes in cells from sensors and signaling systems to effector molecules, to comprehensively analyze the dynamic system of kinases/phosphatases and their substrates and to determine the basic rules of information processing in cells. In this chapter, we describe the protocols necessary to comprehensively and quantitatively measure the phosphorylation-modulated informational networks in cells. The pipeline relies on the selective, quantitative isolation of phosphopeptides generated by the tryptic digestion of complex protein mixtures and their subsequent mass spectrometric and computational analysis. We believe that the protocols and data processing tools described in this chapter will be a valuable resource for biologists interested in the analysis of protein phosphorylation-based signal transduction.
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Evidence ID | Analyze ID | Gene/Complex | Systematic Name/Complex Accession | Qualifier | Gene Ontology Term ID | Gene Ontology Term | Aspect | Annotation Extension | Evidence | Method | Source | Assigned On | Reference |
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Evidence ID | Analyze ID | Gene | Gene Systematic Name | Phenotype | Experiment Type | Experiment Type Category | Mutant Information | Strain Background | Chemical | Details | Reference |
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Evidence ID | Analyze ID | Gene | Gene Systematic Name | Disease Ontology Term | Disease Ontology Term ID | Qualifier | Evidence | Method | Source | Assigned On | Reference |
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Evidence ID | Analyze ID | Regulator | Regulator Systematic Name | Target | Target Systematic Name | Direction | Regulation of | Happens During | Regulator Type | Direction | Regulation Of | Happens During | Method | Evidence | Strain Background | Reference |
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Site | Modification | Modifier | Source | Reference |
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Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Allele | Assay | Annotation | Action | Phenotype | SGA score | P-value | Source | Reference | Note |
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Increase the total number of rows showing on this page by using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; filter the table using the "Filter" box at the top of the table; click on the small "i" buttons located within a cell for an annotation to view further details about experiment type and any other genes involved in the interaction.
Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Assay | Annotation | Action | Modification | Source | Reference | Note |
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Complement ID | Locus ID | Gene | Species | Gene ID | Strain background | Direction | Details | Source | Reference |
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Evidence ID | Analyze ID | Dataset | Description | Keywords | Number of Conditions | Reference |
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