Magnitude of mRNA fold change is best predictor of mRNA-to-protein correlation. Magnitude of mRNA fold change is best predictor of mRNA-to-protein correlation.

Slides:

Advertisements

Similar presentations

Figure S2 A B Log2 Fold Change (+/- cAMP) Transcriptome (9hr)

Advertisements

Additional file 8: Estimation of biological variations

Proteins enriched in HCs are strongly associated with genetic hearing/balance impairment. Proteins enriched in HCs are strongly associated with genetic.

16S rRNA gene abundance and total gene expression of Tannerella species in healthy patient and periodontitis patient samples. 16S rRNA gene abundance and.

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.

Exploration of the data set with age as a continuous variable.

Volume 138, Issue 4, Pages (August 2009)

Fig. 2 Activity-dependent dynamics of β-actin mRNP in neurons from MCP×MBS mouse.(A and B) Examples of β-actin mRNP merge (A) and split (B) events. Activity-dependent.

Fig. 8. Gene and protein changes in ALK-dependent STING pathways in human sepsis. Gene and protein changes in ALK-dependent STING pathways in human sepsis.

Correlation between the ability of Novosphingobium strains from four different habitats to degrade aromatic and xenobiotic compounds. Correlation between.

Integrated protein co‐expression and differential expression across the ALS‐FTD disease continuum Integrated protein co‐expression and differential expression.

Predicted location and functional classification of differentially expressed transcripts. Predicted location and functional classification of differentially.

Titration of antibiotic perturbations results in altered community structures and C. difficile colonization resistance. Titration of antibiotic perturbations.

Fig. 5 Hypoxic tumors from obese mice associate with increased production of IL-6 by adipocytes and myeloid cells. Hypoxic tumors from obese mice associate.

Plots of the number of sequences [log (x + 1) scale] from bacterial OTUs in both PCR replicates (PCR1 and PCR2) of the 348 wild rodents analyzed in the.

Comparison of protein synthesis patterns of L

Correlation of mouse gene expression with bacterial gene expression.

An RpaA-Dependent Sigma Factor Cascade Sets the Timing of Circadian Transcriptional Rhythms in Synechococcus elongatus Kathleen E. Fleming, Erin K. O’Shea

Comparison of the global transcriptomes of nine EPEC isolates.

Cardiac Fibrosis at 18 Weeks Post TAC (A) Representative images (original magnification ×20) of Picrosirius red-stained cardiac tissue sections from HF +

Bacteria significantly correlated with DE miRNAs.

Example usage of mockrobiota MC resource for marker gene and metagenome sequencing pipelines. Example usage of mockrobiota MC resource for marker gene.

The similar shifts of gut microbiota in IBD across cohorts.

Individual genes exhibit distinct stage-specific expression among female gametocytes. Individual genes exhibit distinct stage-specific expression among.

ncRNAs are developmentally regulated as well as mRNAs.

K-Means clustering of protein and mRNA expression patterns after PPAR agonists treatments. k-Means clustering of protein and mRNA expression patterns after.

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.

Four major patterns identified through hierarchical clustering plotted by IPD ratio over time. Four major patterns identified through hierarchical clustering.

Impact of growth phase on the Escherichia coli meltome and proteome

Limited transcriptomic changes upon HOTAIR RNA overexpression in MDA‐MB‐231 breast cancer cells Limited transcriptomic changes upon HOTAIR RNA overexpression.

Renal Fibrosis and Plasma Creatinine Levels at 18 Weeks Post TAC (A) Plasma creatinine levels. (B) Representative images (original magnification ×20) of.

Cecal metabolome during C. difficile colonization and infection.

Log- to stationary-phase growth results in differential acetyl abundance on specific proteins. Log- to stationary-phase growth results in differential.

AZA treatment induces a distinct gene-expression pattern in stromal cells. AZA treatment induces a distinct gene-expression pattern in stromal cells. (A-C)

HOTAIR overexpression has marginal phenotypic and transcriptomic consequences on MDA‐MB‐231 HOTAIR overexpression has marginal phenotypic and transcriptomic.

Trends in metabolite predictability in terms of key gene contributors.

UMOD and ACSM2A expressions correlate with renal function.

Brandon Ho, Anastasia Baryshnikova, Grant W. Brown Cell Systems

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

Exploration of gut and skin microbiome of the habitat switching experiment with Calour. Exploration of gut and skin microbiome of the habitat switching.

Functional potential analyses.

Heat map and hierarchical cluster analysis of the fold changes of genes related to chitin utilization identified in the genome of Vibrio coralliilyticus.

Fig. 1. E-cadherin localizes in nano-scale clusters.

GATC sites where methylation changes over time correspond to a change in gene expression in a dam mutant. GATC sites where methylation changes over time.

Identification of Z-FA-FMK as a potent compound that increases SMN protein expression in HEK293 and patient fibroblast cells. Identification of Z-FA-FMK.

Fig. 5 Hypoxic tumors from obese mice associate with increased production of IL-6 by adipocytes and myeloid cells. Hypoxic tumors from obese mice associate.

Reanalysis of an existing experiment using ADAGE

Changes of other molecular pathways in Msx2 knockout mutant hairs.

Volume 11, Issue 4, Pages (April 2015)

Fig. 4. Impaired induction of TH-response genes in trβ crispants

Heatmaps reveal significantly affected pathways by 4 mg/liter polymyxin B (PMB) in strains PAK and PAKpmrB6 at 1 h using transcriptomics. Heatmaps reveal.

(a) Molecular network clusters of pheophytin and procyanidin and their related metabolites. (a) Molecular network clusters of pheophytin and procyanidin.

Circular plots of 20 regulators reveal redundancies and serial inhibition (10, 12). Circular plots of 20 regulators reveal redundancies and serial inhibition.

IL-27 induces expression of multiple IR by CD8+ T cells.

Using CRISPRi to knock down acm2 expression in L. plantarum WCFS1.

ADCY5 is expressed in isolated human islets and affected by T2D risk alleles. ADCY5 is expressed in isolated human islets and affected by T2D risk alleles.

Overexpression of IL-27 upregulates expression of multiple IR by T cells in vivo. Overexpression of IL-27 upregulates expression of multiple IR by T cells.

Fig. 1 Genes up-regulated in Zic5 KO cells correlate with the increased glycolytic state. Genes up-regulated in Zic5 KO cells correlate with the increased.

K-means clusters of T. elongatus and M

Integrated mRNA and microRNA expression and DNA methylation clusters.

Cell Sorting of Induced SE-like Cells Using SEOR1pro:SEOR1-YFP.

Coexpression of other immune genes with ImSig core signatures.

MAPK/ERK signaling regulates TLR4 gene expression in response to BRAFV600E. MAPK/ERK signaling regulates TLR4 gene expression in response to BRAFV600E.

Hierarchically clustered heat map showing correlations between the relative abundances of microbial species and the levels of volatile compounds in kefir.

Enhanced expression of Cap43 gene by nickel in breast cancer cell lines. Enhanced expression of Cap43 gene by nickel in breast cancer cell lines. Expression.

A and B, linearity of the preamplification step shown by a similar expression pattern of ERα mRNA in four breast tumor samples pre– and post–linear amplification.

Mutational signature analysis of WES data from patients with advanced PDAC. A, Projection of signatures representing four main mutational processes identified.

Fig. 8 Immune correlates of protection.

Differential abundance of metabolites in the sera of HVs and TPs

Small RNA sequencing data quality.

Presentation transcript:

Magnitude of mRNA fold change is best predictor of mRNA-to-protein correlation. Magnitude of mRNA fold change is best predictor of mRNA-to-protein correlation. (A) Protein and mRNA abundances were analyzed at five time points (T1 to T5) from a single culture of “Ca. Pelagibacter ubique.” (B) Protein and mRNA expression of selected genes varied in correlation from −0.93 to +0.99. Error bars at T5 indicate the range of fold changes between the initial (exponential phase) and final (stationary phase) samples from all four control cultures. (C) Plotting all genes according to their protein-to-mRNA correlation throughout the five time points revealed that genes with particularly large changes in mRNA abundance (>eightfold, e.g., osmC) cluster near the high end of the correlation axis, indicating a trend between large mRNA changes and a corresponding change in protein. Point sizes are scaled by y axis position. The same 12 genes are highlighted in panels B and C. *, 0529 and 1265 are abbreviations for genes SAR11_0529 and SAR11_1265. Daniel P. Smith et al. mSystems 2016; doi:10.1128/mSystems.00068-16