Correlations between metabolic pathway abundances and environmental conditions deduced from the ocean samples in this study, at various levels of model.

Slides:

Advertisements

Similar presentations

We Can Read About Mixing Colors

Advertisements

If you say 8 color the ones in your picture purple. If you say 9 color the ones in your picture blue.

Drought in the Western U.S.. Mean US Precipitation (in inches) Average Precipitation in 1 Year (in inches):

Guess the colour Mix the colours Evaluation Group with work.

Tara A.Gianoulis, Jeroen Raes April 13,2010 Presenter: Quan Zhang.

How to detect macromolecules in food

Fig. 1 Map of Europe presenting the three ringing stations (black circles, Hel: Heligoland; Chr: Christiansø; and Jur: Jurmo) and locations of the eight.

Mutant EGFR complexes in lung cancer cell lines and immortalized human bronchial epithelial cells. Mutant EGFR complexes in lung cancer cell lines and.

Schematic representation of investigation into microbial diversity, interactions, and metabolic activity using a combined meta-omic and enrichment culture.

Most promoters preserve their relative activity levels across conditions. Most promoters preserve their relative activity levels across conditions. (A)

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.

Illustration of the reactions and metabolites obtained from random sampling. Illustration of the reactions and metabolites obtained from random sampling.

Average Number of Photons

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

Predicted and measured double‐ring formation.

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.

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

Can I color yellow?. Can I color yellow?

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

Analysis of light spectra.

Clustering and geolocation of ocean samples based on SAR11 phylotype composition. Clustering and geolocation of ocean samples based on SAR11 phylotype.

Hierarchical structure in the yeast transcription regulatory network.

Modules with causal links to ALS are associated with inflammation and enriched with TDP‐43 protein–protein interactions (PPIs)‏ Modules with causal links.

The Mechanism of the Translocation Step in DNA Replication by DNA Polymerase I: A Computer Simulation Analysis Andrei A. Golosov, Joshua J. Warren, Lorena.

What Color is it?.

Hydration and DNA Recognition by Homeodomains

C c Cc is for cat. © ©

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

Validation of some ePTL candidates.

Glucose pulses induce brief, heightened protein and nucleic synthesis in non‐dividing Escherichia coli Glucose pulses induce brief, heightened protein.

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

Volume 4, Issue 5, Pages e5 (May 2017)

Properties of proteins and residues with frequent hotspot mutations

Novel functional roles of uncharacterized genes as functional regulators of cellular cholesterol levels. Novel functional roles of uncharacterized genes.

ncRNAs are developmentally regulated as well as mRNAs.

Volume 108, Issue 7, Pages (April 2015)

PICRUSt analysis results of predicted functional pathways in the gut microbiota. PICRUSt analysis results of predicted functional pathways in the gut microbiota.

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

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

Comparison of proteomics and RNA‐Seq data.

Determination of mRNA synthesis and decay rates.

Submodules of the light yellow module define distinct interneuron classes with common developmental origins. Submodules of the light yellow module define.

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

An integrated NHR network.

Replica Exchange Molecular Dynamics Simulations Provide Insight into Substrate Recognition by Small Heat Shock Proteins Sunita Patel, Elizabeth Vierling,

Design and optimization of the computational model.

Network modules correspond to known and novel functional distinctions between neuronal subtypes. Network modules correspond to known and novel functional.

PKA mediates the primary transcriptional response of cells to glucose.

Community diversity and metagenome depth interact to influence assembly quality. Community diversity and metagenome depth interact to influence assembly.

A multitiered approach to characterize transcriptome structure.

Melting behavior of protein complexes

Volume 114, Issue 1, Pages (January 2018)

Remodeling of the mitochondrial and extracellular proteome during Caenorhabditis elegans aging Remodeling of the mitochondrial and extracellular proteome.

Patterns and regulation of age‐related splicing changes.

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

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.

Contribution of amino‐acid production to the catabolism of BCAAs and AAAs, and to ATP generation under slow‐growing conditions. Contribution of amino‐acid.

Relationship between relative abundance and transcription/abundance ratio (logarithmic scales) of OTUs (brown), ZOTUs (turquoise), and population genomes.

Chze Ling Wee, David Gavaghan, Mark S.P. Sansom Biophysical Journal

Joana Pinto Vieira, Julien Racle, Vassily Hatzimanikatis

Two-way, unsupervised hierarchical clustering representing the 60 tumor cell lines (vertical axis) and the analyzed total, phospho- and cleaved proteins.

Fig. 1 Fractional coverage of the mapping method used in this study.

Presentation transcript:

Correlations between metabolic pathway abundances and environmental conditions deduced from the ocean samples in this study, at various levels of model complexity (see Materials and methods): (A) ‘One‐to‐one’ pairwise correlation (P=0.001) between the abundance of photosystem I genes with average monthly water temperature. Correlations between metabolic pathway abundances and environmental conditions deduced from the ocean samples in this study, at various levels of model complexity (see Materials and methods): (A) ‘One‐to‐one’ pairwise correlation (P=0.001) between the abundance of photosystem I genes with average monthly water temperature. (B) ‘One‐to‐many’ linear model of average monthly water temperature, phosphate concentration and hours of sunlight correlating with carbon fixation gene abundance (R2=0.70). (C) ‘Many‐to‐many’ regularized canonical correlation analysis ordination plot showing the correlation between all environmental variables (text labels; see Materials and methods) and pathway modules (colored dots). The distance between two variables on the plot and their distance from the center point indicates the strength of their correlation and their contribution to explaining the global correlation (i.e., their structural correlation in each dimension given on the respective axes: first dimension, vertical, second, horizontal; see Materials and methods). The overall canonical correlation is high (canonical correlation=0.944 in the first dimension), and the two first dimensions explain 62 and 22% of the total environmental and metagenomic variation, respectively, emphasizing the strong correlation between the climatic factors and functional community composition on the first dimension. Module colors indicate their broad functional classes: yellow, amino acid metabolism; orange, central metabolism; red, energy metabolism, dark green, glycan metabolism; cyan, lipid metabolism; purple, metabolism of other molecules; blue, nucleotide metabolism; brown, replication and repair; light green, transcription; pink, translation; gray, transport system. Highlighted modules are described in more detail in the text. mld, mixed layer depth. Jeroen Raes et al. Mol Syst Biol 2011;7:473 © as stated in the article, figure or figure legend