GIPRCNT

The reponse values in the NCI60 concentration/response screening assay are the count of remaining cells as a percentage of the count of starting cells. By convention these are reported as "GIPRCNT." The "GI" does NOT stand for "G"rowth "I"nhibition.

COMPARE correlations

The sign of the mathematical correlation between two sets of cell line data will be "flipped" if the two sets of data have different "directionality."

"Forward" directionality means that larger numerical values are associated with either greater potency of a compound in the screen or greater expression (quantity or activity). The latter is the case for most data from expression (quantity or activity) studies of the NCI60 cell lines.

"Inverse" directionality means that smaller numerical values are associated with either greater potency of a compound in the screen or greater expression. The former is the case for most NCI60 compound screening data.

Most compound screening results from the NCI60 screen are "inverse." They report compound concentrations as the log10 transform of the concentration in the assay. This applies to the concentration/response data and the endpoint values (GI50, TGI, LC60) that are interpolated from the concentration/response data.

Conversely, most expression assay data from the NCI60 cell lines are "forward." Greater numerical values indicate greater quantity or activity.

The sign of a mathematical correlation is flipped so that the interpretation of a positive COMPARE correlation between NCI60 cell line screening results and expression measurements is: Increasing potency correlates with increasing expression.

To reflect this interpretation visually, the convention for meanGraph presentations of NCI60 screening data is to flip the X axis of the meanGraph so that smaller concentrations are to the right of larger concentrations. The visual interpretation is that more potent compounds (or more sensitive cell lines) have bars further to the right than less potent compounds (or less sensitive cell lines. Expression data are rendered with a standard X axis. Bars for screening results that are positively correlated with expression data will tend to have bars in the same relative directions.