Streptococcus pneumoniae antibiotic stress response

Select one experiment from the dropdown below. Each experiment is labeled as [Strain]-[Condition]-[time (min)]. The strains with a preceding letter in their names are adapted strains (e.g. L-T4 is Levofloxacin adapted TIGR4). The differential expression of each gene will be plotted on the y-axis.

Use this dropdown list to select the x-axis variable. It will be plotted against the differential expression for the selected experiment (y-axis). Tag: functional tag. Category: functional category. Plasticity: variance in expression observed in the GEO dataset. Essential: whether gene is essential, evolvable essential(essential only in some strains) or not. Diameter: cluster diameter (~sequence conservation). Essentiality level: number of strains a gene is essential in. Prevalence: number of strains the gene is present in (=371 for core genes). dW: fitness change (control(no drug)-experiment(drug))

For categorical variables on the x-axis, adding some noise/jitter on the x-axis can be helpful.

Use the brush (draw a rectangle) on the plot to select genes. NOTE: BRUSH DOESN'T WORK WELL WHEN JITTER IS ON

Select two experiments from the dropdown below. Each experiment is labeled as [Strain]-[Condition]-[time (min)]. The strains with a preceding letter in their names are adapted strains (e.g. L-T4 is Levofloxacin adapted TIGR4)

You may choose to color each gene by a feature. Tag: functional tag. Category: functional category. Plasticity: variance in expression observed in the GEO dataset. Essential: whether gene is essential, evolvable essential(essential only in some strains) or not. Diameter: cluster diameter (~sequence conservation). Essentiality level: number of strains a gene is essential in. Diameter: cluster diameter (~sequence conservation). Prevalence: number of strains the gene is present in (=371 for core genes)

Use the brush on the plot to select genes

TIG

PIG

TIG/PIG

Selected

Red Border: Antibiotic target gene

Thick Border: Adapted gene