Analysis of the phosphomimetic ProP‐PD selection results

Slides:

Advertisements

Similar presentations

Microtubule perturbations cause Ste5 patches to form less reliably, delay patch formation, and cause patches to persist for less time Microtubule perturbations.

Advertisements

Tuning the response of the DPI

DNase‐HS sites are main independent determinants of DNA replication timing Simulations based on genome sequence features (GC content, CpG islands), or.

Principles of using neural networks for predicting molecular traits from DNA sequence Principles of using neural networks for predicting molecular traits.

Statistical analysis of the influence of network regulators on topology clusters in the oleate network. Statistical analysis of the influence of network.

Network topology reflects target gene expression profile and function.

binding sites 58 of the 473 unambiguously assigned phosphorylation sites are predicted by Scansite to be sites for binding. 50 of these correspond.

Quantitative proteomics reveals daf‐16‐mediated reduction in protein metabolism in long‐lived daf‐2(e1370) mutants. Quantitative proteomics reveals daf‐16‐mediated.

Sensitivity of RNA‐seq.

Motif detectability corresponds to the phylogenetic profile of the cognate transcription factor. Motif detectability corresponds to the phylogenetic profile.

Impact of systematic kinase and phosphatase k. o. on M

Distribution of summed MS1 intensities

Heatmaps of the gene mutation distributions in oncogene‐signaling blocks for six representative cancer types. Heatmaps of the gene mutation distributions.

Functional assays confirm daf‐2‐dependent reduction in protein metabolism. Functional assays confirm daf‐2‐dependent reduction in protein metabolism. (A)

Functional analysis of duplicate pair CIK1–VIK1 (A) Genetic interaction profile similarity. Functional analysis of duplicate pair CIK1–VIK1 (A) Genetic.

Proteins with hotspot mutations are often in the interaction networks with known cancer driver proteins Proteins with hotspot mutations are often in the.

(C–F) Complete interaction networks (representing both baits and preys) for selected groups of baits. (C–F) Complete interaction networks (representing.

Evaluating other shRNA data and methods.

A complete functional map of UBE2I

Confirmation of pool data with isogenic culture

Disease‐causing mutations influence the association of CSPα with partner proteins Disease‐causing mutations influence the association of CSPα with partner.

Correlating protein to mRNA and proteins per mRNA ratios

Identification of MOSPD2, a new FFAT motif‐binding protein

Network derived from large‐scale fractionation predicts 48 protein complexes and communities Network derived from large‐scale fractionation predicts 48.

Characterization of promoters relative to pAGA1

Genomic profiling of fitness in periodic salt stress

Phosphosite mutations in TP53 correlate with increased patient survival. Phosphosite mutations in TP53 correlate with increased patient survival. (A) ActiveDriver.

Heat maps showing global relative growth phenotype and comparison between measured and predicted values. Heat maps showing global relative growth phenotype.

Identification of essential genome features.

Alignment time for Clustal Omega (red), MAFFT (blue), MUSCLE (green) and Kalign (purple) against the number of sequences of HomFam test sets. Alignment.

Direct dFOXO targets in wild‐type adult flies.

Validation of some ePTL candidates.

The transcript profiles in the three human cell lines based on RNA sequencing (RNA‐seq). The transcript profiles in the three human cell lines based on.

Homologous recombination deficiency scores correlate with drug‐induced cell death in primary ovarian cancer cells Homologous recombination deficiency scores.

Detailed analysis of post‐translational compensation of varying Erk concentration. Detailed analysis of post‐translational compensation of varying Erk.

Visualization of a global auxin‐response gradient in the root meristem

Dynamic changes of protein phosphorylation identify ERK1/2 substrates from cytosolic and nuclear compartments. Dynamic changes of protein phosphorylation.

The LuTHy procedure The LuTHy procedure Schematic representation of the workflow of the LuTHy method. Expression vectors encoding NL and PA‐mCit‐tagged.

Collective shifts of abundance for nuclear and extracellular proteins in colorectal cancer Collective shifts of abundance for nuclear and extracellular.

Phenotypic profiling by between‐well comparison of feature profiles

HMGB1 reverses mitochondrial DNA damage caused by mutant Atxn1 The mitochondrial DNA amplification assay with cerebellar tissue revealed that mitochondrial.

Recursive construction and error correction of a simple combinatorial library. Recursive construction and error correction of a simple combinatorial library.

Transcriptomic and epigenetic changes associated with Factor 1 in the scMT data Transcriptomic and epigenetic changes associated with Factor 1 in the scMT.

Categorizing cell type‐specific auxin responses.

Comparison of nuclear surface area of HeLa and RKO cells

Impact of growth phase on the Escherichia coli meltome and proteome

Simulation showing that the cell length variability of the entire population can mask abnormal cell length variability at a specific cell cycle period.

Transformation of expression data to identify more direct consequences of perturbation Expression changes under amino acid starvation conditions (30 min,

Antibody analysis of Erk.

Subnetworks enriched for the hallmarks of cancer.

Stage‐dependent diurnal transcript changes.

Identification of a new cryptic lipid‐binding domain in Ecm25.

WES identification of heterozygous compound mutations in ALPI

Melting behavior of protein complexes

Characterising dermis expansion and gene expression changes during mouse development (related to Fig 1)‏ Characterising dermis expansion and gene expression.

Dynamic transcriptome analysis in yeast.

Antisense expression associates with larger gene expression variability. Antisense expression associates with larger gene expression variability. (A–D)

WES identification of heterozygous compound mutations in ALPI

Competence initiation during the progression to spore formation.

Mass spectrometric validation of DLG5 as a CDKL5 substrate

Scribble PDZ1 preferentially interacts with p‐1 and p‐3 phosphorylated ligands as shown by affinity determinations (MST and ITC), NMR structure, mutational.

PRG‐1R346T: loss‐of‐function mutation reduced LPA internalization due to altered O‐glycosylation PRG‐1R346T: loss‐of‐function mutation reduced LPA internalization.

(A) Observed significant protein fold‐changes during the fed–fasting transition in C57BL/6J (B6) and 129Sv (S9) mice fed with a normal diet (T0). (A) Observed.

Many of the diseases associated with high coevolution scores share genetic components. Many of the diseases associated with high coevolution scores share.

Diagram of the workflow (related to Fig 1)‏

Intestinal differentiation is coupled with global rewiring of gene expression Intestinal differentiation is coupled with global rewiring of gene expression.

Fraction of flux entering the PEP‐glyoxylate cycle as a function of hexose uptake rate in batch (A) and chemostat (B) cultures. Fraction of flux entering.

Ankyrin domain residues permit activation of LRRK2 by Rab29

Lucy R. Forrest, Christopher L. Tang, Barry Honig Biophysical Journal

Predicted pathogenic BRCA1 amino acid substitutions are confined to the evolutionarily conserved N- and C-terminal domains. Predicted pathogenic BRCA1.

Presentation transcript:

Analysis of the phosphomimetic ProP‐PD selection results Analysis of the phosphomimetic ProP‐PD selection results Fractions of the sequencing counts for individual peptides (wild‐type peptides indicated by red bars and phosphomimetic variants by blue bars) from NGS analysis of binding‐enriched phage pools from selections against the PDZ domains of Scribble and DLG1. Peptides are sorted based on the site of the phosphomimetic mutations (corresponding to known or putative phosphosites). Standard deviations are indicated (n = 3 for all cases except for Scribble PDZ2 where n = 2). Peptide pairs for which there are significant differences between the fractions of NGS counts for wild‐type and phosphomimetic peptides are indicated with * (multiple t‐tests, significance level 0.05). Peptides with multiple phosphorylation sites have been omitted from this analysis for clarity. For further details, see Table EV3.Position weight matrices (PWMs, WebLogo3) representing the phosphomimetic ProP‐PD selections data for the PDZ domains of Scribble and DLG1. The numbers of peptides used for the analysis are indicated.Scoring matrices of the effects of phosphomimetic mutations on the phosphomimetic ProP‐PD results of the PDZ domains of Scribble and DLG1. Scores are calculated from the ratios between NGS counts of the phosphomimetic peptides and the sum of the NGS counts of the wild‐type and phosphomimetic peptides. A score of 0 (red) indicates that the selection was dominated by wild‐type peptides, and a score of 1 (blue) indicates that the selection was dominated by peptides with phosphomimetic mutations at the given position (n = 3 for all cases except for Scribble PDZ2 where n = 2). Positions marked with * have a score that is significantly different from the score 0.5 of a neutral effect as determined using multiple t‐tests and correcting for multiple comparisons using a false discovery rate of 2.5%. The position for which only wild‐type or phosphomimetic peptides are represented in the data set could not be subjected to this test. Gustav N Sundell et al. Mol Syst Biol 2018;14:e8129 © as stated in the article, figure or figure legend