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leskia29 / group_2

Associations among independent variables: Create summaries and visualizations of how the independent variables are associated with each other. Here, many of the characteristics of the drugs might be associated with each other, and the drugs might “cluster” into groups based on these characterstics. This group will need to come up with ways (and code) to analyze that in the data. This might include correlation plots, hierarchical cluster analysis, and principal components analysis.
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Meanings of column names for in vitro drug measurements #1

Open geanders opened 6 years ago

geanders commented 6 years ago

@lyonsm7: Do you know what the full names should be for each of the following columns in the summary datasheet?

We've got the definitions of all the mouse measurements at the bottom of the Excel sheet, but not the explanations for those (although we do have units).

lyonsm7 commented 6 years ago

These are all properties of the drug

cLogP: octanol:water partition coefficient. This is the logarithm of the concentration of drug in octanol (oil) and water - it's a measure of lipohilicity/hydrophoicity of the drug.

huPPB: human plasma protein binding. The fraction of drug concentration that binds to plasma proteins. (1 - huPPB) is then the free concentration of the drug. muPPB: mouse plasma protein binding.

MIC_Erdman: minimum inhibitory concentration Erdman strain. This is the minimum drug concentration that inhibits the growth of the bacteria. In this case the Erdman strain of Mycobacterium tuberculosis. MIC_Rv: MIC for H37Rv strain of M. tuberculosis.

Caseum_binding: fraction of drug concentration that is bound to the constituents of the caseum (caseum is at the center of the necrotic granuloma)-

MacUptake - rate of uptake of drug molecules by macrophages. I'm not sure of the units.

geanders commented 6 years ago

Perfect, thanks so much @lyonsm7!

geanders commented 6 years ago

Also, from looking at the Excel sheet, it looks like MacUptake is unites (I / E concentration ratio-- no units if it's a ratio, right?).

lyonsm7 commented 6 years ago

I think yes - this could refer to concentrations inside and outside the macrophage I intracellular / E extracellular . the time at which the measurement is taken is probably a standard one.