Re: Stanley's ICA, Intensity Correlation Analysis; ICQ, Intensity Correlation Quotient

Posted by EliseStanley on Mar 16, 2014; 8:58am
URL: http://imagej.273.s1.nabble.com/Stanley-s-ICA-Intensity-Correlation-Analysis-ICQ-Intensity-Correlation-Quotient-tp5006871p5006939.html

Hi Jeremy,

Everyone is looking for a single value to declare whether two proteins associate. The sad truth is that this is almost always not possible because even proteins proteins that associate reliably - such as myosin and actin, say, may do not do so in some regions of the cell - such as during synthesis and transport.  Worse, some proteins are generally in different locations and only associate transiently - at the point where they are of most interest.  An example would be a protein on a secretory granule that is involved with exocytosis.

Thus, the obsession with single-value association units is fraught with problems from the start.

Intensity correlation analysis was invented to permit the investigator to detect where proteins vary in synchrony in the cell - and for that the scalar, not the discrete (yes or no staining) value is used.  The result is a plot within which it is possible to detect quantitative correlations of immunostaining and it is also possible (though most analysis methods do not yet take advantage of this) to go back to the original image and identify where in the cell the two proteins associate and where they do not.  

When I invented that method I realized that elegant as the ICA method is, statistical comparisons between treatments required a way to get a single-value estimate of whether the two proteins associate.  That's the origin of the ICQ - it really throws away 99% of the (spatial) information in the ICA analysis for the sake of a simple statistically testable single value output.  And yes, this is not perfect!  I suppose we could have a subroutine that allowed you to calculate the ICQ values in select regions of the cell - I think that would be amazing.  I had hoped that a commercial software vendor would have picked up on what I think is an astonishing potential of ICA analysis in two or three dimensions.  Unfortunately, that has not happened.  

I hope you have looked at the original paper in which most of these issues are discussed.  But ICA analysis and the ICQ value are unrelated to Pearsons - and I maintain that the latter is invalid because of how it handles random staining vs negative-correlated staining.  Further, it is not possible to pull out covariance within subregions of your sample.

ee