Feature‐based COG enrichment analysis

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

GFP‐Sed5p localization defect in sgt2Δ.

Growth rate‐dependent gene expression under glucose limitation.

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

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.

Overview of the experimental setting.

Melting behavior of protein complexes

(A) gToW growth phenotypes occur in the absence of leucine, and red squares indicate a significant growth‐rate defect as compared with the empty plasmid.

Usage of l‐carnitine antimetabolites for the treatment of HCCl‐Carnitine and metabolites in the l‐carnitine biosynthetic pathway, as well as two essential.

Hnf4g importance in human colon cancer organoids and regulation of the Hnf4a locus Hnf4g importance in human colon cancer organoids and regulation of the.

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.

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

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

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.

Structure of in‐frame deletions.

Comparative analysis of RNA and protein profiles.

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

Confirmation of pool data with isogenic culture

Splicing changes in development and aging.

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

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

Correlating protein to mRNA and proteins per mRNA ratios

Coupling immunophenotypes to Drop‐seq data

Characterization of promoters relative to pAGA1

Hierarchical structure in the yeast transcription regulatory network.

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

Direct dFOXO targets in wild‐type adult flies.

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.

Experimental approach and reproducibility

Multi‐Omics Factor Analysis: model overview and downstream analyses

Phenotypic profiling by between‐well comparison of feature profiles

Diversity of methods utilized to model neurological diseases using patient‐derived iPSCs Diversity of methods utilized to model neurological diseases using.

Effect of the loss of Kar4 on the induction of various promoters

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

Characterization of Factor 5 (oxidative stress response factor) in the CLL data Characterization of Factor 5 (oxidative stress response factor) in the.

Dynamics and expression level of mating‐dependent promoters

CRISPR knockdown can be multiplexed to modulate expression of two genes without cross‐talk CRISPR knockdown can be multiplexed to modulate expression of.

Shared components define the ‘ancient’ phagosome.

Neurogenins induce a network of transcription factors that mediate iNGN neurogenesisA network of transcription factors involved in iNGN neurogenesis was.

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

QRT–PCR analysis of tissue‐specific candidate gene expression in response to reduced IIS qRT–PCR analysis of tissue‐specific candidate gene expression.

Allele‐specific expression at single‐cell resolution

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.

Comparison of proteomics and RNA‐Seq data.

Impact of growth phase on the Escherichia coli meltome and proteome

Determination of mRNA synthesis and decay rates.

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,

An integrated NHR network.

Classification of the 1458 identified proteins into molecular functions. Classification of the 1458 identified proteins into molecular functions. The pie.

Subnetworks enriched for the hallmarks of cancer.

Proliferative advantage depends on environmental dynamics

Stage‐dependent diurnal transcript changes.

When grown with biofuel, strains with beneficial pumps dominate the culture. When grown with biofuel, strains with beneficial pumps dominate the culture.

Melting behavior of protein complexes

Examples of differentiating humoral response features identified by classification models Examples of differentiating humoral response features identified.

Experimental validation of predicted endocytosis functions in human.

Global and focused views of human interaction map.

Functional metabolic rearrangements in chloramphenicol‐resistant populations Functional metabolic rearrangements in chloramphenicol‐resistant populations.

Interaction of Gpr1/Gpa2 and Sch9.

Occurrence of fur−-only genes and expected sensitivity to Fur.

(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.

Sequence dependence of Met4 recruitment.

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

Metabolic differences in the small intestine AMetabolic genes as well as the associated reactions involved in the formation of glutathione (GSH) are presented.B,

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.

Presentation transcript:

Feature‐based COG enrichment analysis Feature‐based COG enrichment analysis Pie charts representing, on a feature‐by‐feature basis, the relative distribution of COG categories among the gene deletion strains associated with s ≥ 3. The enriched COG categories are labeled and highlighted with an exploded pie sector. The under‐represented COG categories are further highlighted by an asterisk. Enrichments and under‐representations with an associated (FDR‐corrected) q‐value < 0.05 were considered significant. Only morphological and growth features with at least one enriched or under‐represented COG category are represented.Same as in (A) but for s ≤ −3. Manuel Campos et al. Mol Syst Biol 2018;14:e7573 © as stated in the article, figure or figure legend