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Results: 7

1.
Fig. 4.

Fig. 4. From: Integrated Phosphoproteomics Analysis of a Signaling Network Governing Nutrient Response and Peroxisome Induction.

Detection of known signaling pathway proteins. Pathways identified in the literature were compared with proteins that were detected by mass spectrometry-based phosphoproteomics analysis.

Ramsey A. Saleem, et al. Mol Cell Proteomics. 2010 September;9(9):2076-2088.
2.
Fig. 1.

Fig. 1. From: Integrated Phosphoproteomics Analysis of a Signaling Network Governing Nutrient Response and Peroxisome Induction.

Work flow for isolation and integration of phosphopeptides into signaling networks. SILAC, stable isotope labeling with amino acids in cell culture.

Ramsey A. Saleem, et al. Mol Cell Proteomics. 2010 September;9(9):2076-2088.
3.
Fig. 3.

Fig. 3. From: Integrated Phosphoproteomics Analysis of a Signaling Network Governing Nutrient Response and Peroxisome Induction.

Specific subsets of phosphoproteome enriched from cells incubated in oleic acid- or glucose-containing medium. A, comparison of the number of unique phosphopeptides, the number of phosphoproteins, and the number of unique phosphoproteins for oleic acid-enriched, glucose-enriched, and non-enriching phosphopeptides. B, Venn diagram showing the overlap between identified proteins with peptides increasing in phosphorylation in oleic acid and those proteins with peptides increasing in phosphorylation in glucose. C, subcellular localizations for proteins enriched in either oleic acid or glucose. D, functional annotations of the proteins as a kinase or phosphatase (Signaling), a transcription factor, or other. ER, endoplasmic reticulum.

Ramsey A. Saleem, et al. Mol Cell Proteomics. 2010 September;9(9):2076-2088.
4.
Fig. 5.

Fig. 5. From: Integrated Phosphoproteomics Analysis of a Signaling Network Governing Nutrient Response and Peroxisome Induction.

Quantitative PCR reveals a role for oleate-enriched phosphorylation of Pip2p and Cst6p. A, yeast cells carrying a S783A-mutagenized version of Pip2p were tested for expression of oleate-responsive loci POT1, CTA1, FOX2, and POX1. Shown are the levels of induction after 30 min in oleate-inducing medium. By 90 min, the differences between wild type and the Pip2p S783A strain were not significant (data not shown). B, at 90 min of oleate induction, increased expression of oleate-responsive loci (POT1, CTA1, FOX2, and POX1) is detected in the two Cst6p mutagenized strains. Cst6-1 is multiply mutated (S396A,S399A,T401A), whereas Cst6-2 is singly mutated (T401A). Error bars show the standard deviation.

Ramsey A. Saleem, et al. Mol Cell Proteomics. 2010 September;9(9):2076-2088.
5.
Fig. 6.

Fig. 6. From: Integrated Phosphoproteomics Analysis of a Signaling Network Governing Nutrient Response and Peroxisome Induction.

FA signaling network. Integrated network of enriching phosphoproteins, signaling proteins known to regulate responses to FAs, and regulatory proteins. Proteins are indicated by nodes, and protein-protein interactions are shown by edges between the nodes. Green nodes indicate enrichment in oleic acid, red nodes indicate enrichment in glucose, blue nodes indicate enrichment of different sites in glucose and oleic acid, and white nodes indicate no information on phosphorylation status. The node border indicates the role of the protein as a positive (red), negative (green), or neutral (gray) effector of expression of FA-responsive loci. Diamond-shaped nodes indicate kinases, parallelogram-shaped nodes indicate phosphatases, octagonal nodes indicate regulators, circular nodes indicate transcription factors, and rounded rectangular nodes indicate phosphorylation substrates. The network is provided as a Cytoscape file (supplemental FA_Net_Saleem_MCP.cys) to facilitate interactive viewing.

Ramsey A. Saleem, et al. Mol Cell Proteomics. 2010 September;9(9):2076-2088.
6.
Fig. 2.

Fig. 2. From: Integrated Phosphoproteomics Analysis of a Signaling Network Governing Nutrient Response and Peroxisome Induction.

Fractionation and analysis of phosphoproteome. A, HILIC fractionation of tryptic peptides retains phosphopeptides until later in the elution profile. Chromatographic traces at 214 (black) and 280 nm (gray) and the gradient profile are shown with the percentage of Solvent A (“Experimental Procedures”) indicated above the gradient. Pools of the HILIC-based fractionation for IMAC-based enrichment of phosphopeptides are shown on the x axis. Combined Fractions 8, 9, and 10 have the highest percentage of phosphopeptides. B, Venn diagram of the number of non-redundant peptides identified by MS2- and MSA-based mass spectrometry. The majority of the phosphoproteome can be identified by MS2 analysis alone. C, number of phosphorylation sites (N Phos) per peptide. The majority of the peptides identified were doubly phosphorylated (60%).

Ramsey A. Saleem, et al. Mol Cell Proteomics. 2010 September;9(9):2076-2088.
7.
Fig. 7.

Fig. 7. From: Integrated Phosphoproteomics Analysis of a Signaling Network Governing Nutrient Response and Peroxisome Induction.

Network analysis. Top, the most highly connected nodes are the nodes that tend to exert the greatest effect on the expression of FA-responsive loci. The x axis indicates proteins from the network for which there are data on the role of the protein in expression of FA-responsive loci. The y axis is the normalized score for connectivity with 1 indicating the most highly connected node in the network. The red line indicates node connectivity (connectivity norm), whereas the blue line (deletion effect norm) indicates the role of the network protein as a negative effector (positive score on the y axis) or positive effector (negative score on the y axis) of the FA response. Middle, most nodes in the network have few connections. The x axis indicates the number of connections (k); the y axis indicates the number of nodes with a given number of connections (P(k)). Bottom, the degree of distribution of the FA network follows the power law. The x axis is the log10 of connectivity (k); the y axis represents the log10 of the number of nodes in a given bin (P(k)). Each red dot represents a given number of connections (k) from the x axis of the middle panel. This connectivity shows that this network has topology consistent with scale-free networks.

Ramsey A. Saleem, et al. Mol Cell Proteomics. 2010 September;9(9):2076-2088.

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