Validation of the CCE associations by mass spectrometry.

Slides:

Advertisements

Similar presentations

Abundance of proteins matching selected subcellular locations and functions in CaCo‐2 cells. Abundance of proteins matching selected subcellular locations.

Advertisements

Schematic diagram of the three circuits analysed in this work.

Linear Regression.

A kinetic model reconciles observed ERK phosphorylation, localization, and activity responses A Schematic of a simple kinetic model including cytosolic.

Melting behavior of proteins identified in the Escherichia coli meltome and their properties Melting behavior of proteins identified in the Escherichia.

Thermal proteome profiling in Escherichia coli

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.

Analysis of in silico flux changes along the exponential growth phase: (A) In silico flux changes from 24 to 36 h, from 36 to 48 h, and from 48 to 60 h.

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

Data analysis of thermal proteome profiling

Hypothetical example of co‐complex interactions being scored by weighted matrix model Hypothetical example of co‐complex interactions being scored by weighted.

Epistatic interactions and gene expression variation.

Exo‐metabolomics profiling of major metabolites elucidated the metabolic capabilities of monospecies Exo‐metabolomics profiling of major metabolites elucidated.

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

Dual allele labeling reveals a trans‐acting source for extrinsic noise

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.

Mononucleotide models describe sequence‐to‐shape relationships well

The TBON model. The TBON model. (A) Representative confocal images of E14Tg2A cells stained for Tcf3 (green), Nanog (red), Oct4 (magenta), and total β‐catenin.

Comparative analysis of RNA and protein profiles.

Highly correlating interaction profiles can predict functional similarity Highly correlating interaction profiles can predict functional similarity AROC.

Large‐scale image‐based CRISPR‐Cas9 gene perturbation profiling

Buffering of non‐functional mRNA co‐regulation likely is a passive process Buffering of non‐functional mRNA co‐regulation likely is a passive process Percentage.

Model training of generalized Lotka–Volterra (gLV) to time‐resolved measurements of monospecies and pairwise assemblages Model training of generalized.

Luminex phosphorylation measurements are reproducible and have broad dynamic range Individual difference in insulin‐induced phosphorylation of ERK measured.

Correlating protein to mRNA and proteins per mRNA ratios

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

Networks of ERK substrates.

Validation of some ePTL candidates.

Compartment‐specific analysis reveals differences in organelle composition that can be validated by sub‐cellular fractionation Compartment‐specific analysis.

Examples for intrachromosomal mRNA co‐regulation patches

Titrations of other division proteins support FtsZ as the division limitation Titrations of other division proteins support FtsZ as the division limitation.

Mean feature profiles of targeted cells are highly consistent between gRNA sequences Mean feature profiles of targeted cells are highly consistent between.

Systematic analysis of interacting proteins with known binding affinities Systematic analysis of interacting proteins with known binding affinities Selection.

Validation of proteins identified by mass spectrometry.

Patient organoids respond more diverse to drugs and with lower therapeutic potential than 2D cultured patient cells Patient organoids respond more diverse.

Small‐molecule‐driven cell‐type enrichment as a model for intestinal differentiation Small‐molecule‐driven cell‐type enrichment as a model for intestinal.

DeathPro dyes Hoechst and PI do not affect organoid growth and drug responses DeathPro dyes Hoechst and PI do not affect organoid growth and drug responses.

Shared components define the ‘ancient’ phagosome.

Francis Crick's central dogma of biology revolves around the transcription of mRNA from DNA, the translation of proteins from mRNA, and the degradation.

Antisense transcription, measurement, and correction

Evaluation of assay performance with positive and negative binary reference sets Evaluation of assay performance with positive and negative binary reference.

Two‐way unsupervised uncentered unnormalized hierarchical clustering using a Pearson's correlation of the phenotypic profiles of 4281 nonessential genes.

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

48 clinically relevant GPCR receptors mapped using MYTH

Comparison of proteomics and RNA‐Seq data.

Characteristics of tissue‐specific co‐expression networks (CNs)‏

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.

Kinome‐wide activity regulation derived from known substrates and 41 quantitative phosphoproteomic studies Kinome‐wide activity regulation derived from.

An integrated NHR network.

Subnetworks enriched for the hallmarks of cancer.

Reproducibility of DeathPro drug screens

Maintenance metabolism alone cannot explain non‐division

Melting behavior of protein complexes

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

Experimental validation of predicted endocytosis functions in human.

Drug sensitivity described by LD50 is similar in cells cultured in 2D or as organoids Drug sensitivity described by LD50 is similar in cells cultured in.

Global and focused views of human interaction map.

Functionality of smORFs Venn diagram showing the number of smORF proteins identified by MS in different experiments. Functionality of smORFs Venn diagram.

Correlation of flux and enzyme concentration (inferred from transcripts) changes for reactions in central metabolism. Correlation of flux and enzyme concentration.

Integration of proteomic data into the model

Proteomic analysis of human transcription factors Disease correlation of 19 TFs and 4 well‐studied FOX family members, based on their GO annotations. Proteomic.

CRISPR‐Cas9 gene perturbation profiling in HeLa cells

BRI1 signaling at the dividing cells restores overall root growth

Tissue specificity and the human protein interaction network

Comparison of 16S sequencing and shallow shotgun recovery of species-level taxa. Comparison of 16S sequencing and shallow shotgun recovery of species-level.

Presentation transcript:

Validation of the CCE associations by mass spectrometry. Validation of the CCE associations by mass spectrometry. (A) Between 49 and 59% of the 7000 CCE associations correspond to true physical associations, as estimated with shotgun proteomics elution profiles. The extent of co‐elution of positive control (literature; Joshi‐Tope et al, 2005), negative control (random), and CCE associations were calculated as the Pearson correlation coefficients between interaction partners’ elution profiles, defining a correlation coefficient histogram for each set of associations. The proportion of true positives in the 7000 CCE associations was estimated by fitting the CCE correlation coefficient histogram as a linear mixture of the control histograms, with the true‐positive rate corresponding to the percentage of the positive control histogram providing the best fit (inset). (B) Specific examples of correlated elution profiles for CCE partners, supporting the physical association of these protein pairs. Arun K Ramani et al. Mol Syst Biol 2008;4:180 © as stated in the article, figure or figure legend