Putative targets of miRNAs directly induced by p53 with down-regulated mRNA- and de novo protein synthesis or reduced de novo protein synthesis only. Putative.

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binding sites 58 of the 473 unambiguously assigned phosphorylation sites are predicted by Scansite to be sites for binding. 50 of these correspond.
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Sequence alignment of C-terminal phosphorylated plant aquaporins
Distribution of disorder in the cytosolic phosphoproteome
Phosphorylation and sequence disorder in microtubule-associated protein Tau.A, schematic illustration of the domain profile of Tau with all known phosphorylation.
Distribution of phosphorylation sites identified in the cytosolic phosphoproteome.A, numbers of approved phosphopeptides, previously phosphorylated peptides,
Microvesicles released by PC-3 cells.
Analysis of CD151 and CD147 as potential prostate cancer biomarkers.
Percentage of proteins identified in envelope membrane extracts according to the purification method and the number of transmembrane domains. Percentage.
Differential conjugation of endogenous SUMO-1 and endogenous SUMO-2/3 to target proteins.A and B, SUMO-1 and SUMO-2 proteins were produced in E coli and.
Plasma CEP adducts and autoantibodies by donor age.
Frequency distribution of the GRAVY of the theoretical proteins (open bars) and of 110 genes encoding proteins identified on a 2-D electrophoresis gel,
Time course of phosphorylation changes at Ser-293, Ser-300, and Ser-232 in PDHE1α following kinase inhibition with DCA. A, relative quantitation over three.
Two-dimensional electrophoresis results and validation with Western blotting. Two-dimensional electrophoresis results and validation with Western blotting.
Distributions of the ELDP values and Mascot scores for all protein identifications.a, frequency of ELDP value returned by correct (gray bars) and incorrect.
Significantly enriched phosphorylation motifs from up-regulated phosphopeptides by Motif-X analysis. Significantly enriched phosphorylation motifs from.
Visual validation of the computational outputs.
Epitope Mapping Performance using a single peptide microarray.
Frequency distribution of the effect size measure (ESM) of sperm protein spots of type-1 diabetic (A), type-2 diabetic (B) and non-diabetic obese (C) patients.
Novel p53 target genes identified by RNA-Seq, pSILAC and ChIP-Seq.
Assay of NOS activity. Assay of NOS activity. Box show total NOS activity, the calcium-dependent activity of the constitutive isoforms of NOS (eNOS and.
Membrane protein overexpression affects the pH of the culture and protein secretion.A, the pH of the culture of GFP fusion-overexpressing cells and the.
Bottom-up proteomic characterization of MALDI IMS samples.
Genome-wide analysis of p53 occupancy.
Representative example of LAXIC performance for complex plant phosphoproteome. Representative example of LAXIC performance for complex plant phosphoproteome.A.
Success rates in validation of antibodies from external providers
Results from the Morris water task.
Technical reproducibility and biological variability.
Identification of de novo synthesized UPF1 target proteins.
NanoLC-MS/MS/based analysis of proteome differences between colonospheres and isogenic differentiated tumor cells. NanoLC-MS/MS/based analysis of proteome.
The evolutionary conservation of the phosphoproteomes.a, E. coli. b, B. subtilis. The evolutionary conservation of the phosphoproteomes.a, E. coli. b,
Colonopshere-enriched proteins display functional interactions.
Identification of SUMO3peptides from 2D-LC-MS/MS analyses of a tryptic digest of HEK293-SUMO3 cells using DDA and DIA methods. Identification of SUMO3peptides.
Proteins previously reported in published MALDI IMS studies and their frequency of observation in the present study. Proteins previously reported in published.
Schematic model of effector pathways that mediate tumor suppression by p53. Schematic model of effector pathways that mediate tumor suppression by p53.
MRNAs that show increased protein synthesis following UPF1 depletion are enriched for those with very long 3′UTRs. mRNAs that show increased protein synthesis.
Molecular network analysis of up-regulated genes and proteins in NF1-KD PC12 cells. Molecular network analysis of up-regulated genes and proteins in NF1-KD.
High correlation of expression changes of NMD-regulated genes identified by both the pSILAC screen and previously reported global RNA screens after UPF1.
Analysis of newly synthesized proteins by combined pulsed SILAC and click chemistry enrichment. Analysis of newly synthesized proteins by combined pulsed.
Schematic summarizing the various functions and features of MASH Suite Pro. Schematic summarizing the various functions and features of MASH Suite Pro.
Protein microarrays for validation of antibodies.
Validation of p53- and miRNA-mediated down-regulation
Testing the effectiveness of the three-step peptide fractionation method.A, μLC mass chromatograms of SCX fractions for an acidic FFE fraction. Testing.
Altered pathways in prostate cancer.
Interaction networks of the regulated phosphoproteins.
The PPAR-α agonist GW7647 reduces experimentally induced myopia.
Identification of chaperonin GroEL (Rv0440) with representative MS/MS spectrum. Identification of chaperonin GroEL (Rv0440) with representative MS/MS spectrum.A,
Plot of the deviation of the predicted pI value of every peptide spectrum from the average pI calculated for each fraction for validated (a) and non-validated.
Distribution of the phosphoproteins based on GO analysis, including biological process (Left) and cellular component (Right). Distribution of the phosphoproteins.
A, Absolute ion intensities of m/z 322, 922 and 1522 as function of the transfer time. A, Absolute ion intensities of m/z 322, 922 and 1522 as function.
Examples of protein that display profiles corresponding to GO/GROW and STOP signals.A, example of STOP profile: normalized spot volume profile of apoA-I.
K-Means clustering of protein and mRNA expression patterns after PPAR agonists treatments. k-Means clustering of protein and mRNA expression patterns after.
Immuno-MS results from antibodies toward 20 different target proteins in HeLa cell lysates. Immuno-MS results from antibodies toward 20 different target.
Transcriptionally regulated genes in Δsaci_ptp and Δsaci_pp2a as compared with the strain MW001. Transcriptionally regulated genes in Δsaci_ptp and Δsaci_pp2a.
Bar plot representation of the transcriptomic changes in Δsaci_ptp and Δsaci_pp2a. Bar plot representation of the transcriptomic changes in Δsaci_ptp and.
Localization of selected clones in mammalian COS-7 cells.
Biochemical characterization of the protein phosphatases Saci-PTP.
Voronoi treemaps (109) comparing protein expression profiles of M
Changes in mRNA levels do not correlate with changes in protein levels in upf1Δ and xrn1Δ cells. Changes in mRNA levels do not correlate with changes in.
A simplified example of a protein summary list.
Classification of the 1458 identified proteins into molecular functions. Classification of the 1458 identified proteins into molecular functions. The pie.
Separation of colonospheres from differentiated tumor cells by cluster analysis. Separation of colonospheres from differentiated tumor cells by cluster.
Enlargements of 2-D gels visualized by Coomassie Brilliant Blue staining. Enlargements of 2-D gels visualized by Coomassie Brilliant Blue staining. In.
Western blotting analysis of purified cytoplasmic membranes.
Overlap between changes in de novo protein synthesis after p53- or miR-34a-induction. Overlap between changes in de novo protein synthesis after p53- or.
GeneGoTM-based signaling pathway annotations of proteins identified in CD56+ NK cell subsets. GeneGoTM-based signaling pathway annotations of proteins.
Statistical evaluation of CD56+ NK cell subset data.
Changes in protein expression during distinct stages of NK cell differentiation. Changes in protein expression during distinct stages of NK cell differentiation.
The average median S.D. and PEV reduction after applying different normalization methods compared with raw data. The average median S.D. and PEV reduction.
Occurrence of fur−-only genes and expected sensitivity to Fur.
Differential protein, mRNA, lncRNA and miRNA regulation by p53.
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Putative targets of miRNAs directly induced by p53 with down-regulated mRNA- and de novo protein synthesis or reduced de novo protein synthesis only. Putative targets of miRNAs directly induced by p53 with down-regulated mRNA- and de novo protein synthesis or reduced de novo protein synthesis only. Predicted miRNA targets with (A) down-regulated mRNA- and de novo protein synthesis, (B) reduced de novo protein synthesis only are displayed. Known miRNA targets are underlined and targets experimentally validated in this study are marked with a black arrow. Proteins that showed a heterogeneous distribution of fold changes in independent experiments (class II candidates, see Experimental procedures) are marked with an asterisk (*). Sabine Hünten et al. Mol Cell Proteomics 2015;14:2609-2629 © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.