Hello,

Our lab is currently looking at patterns of expression for genes involved in reading single words. We have RT-PCR data on several genes interrogated in 18 areas of human brain. We would like to present these data projected on a 3-D representation of the brain (perhaps a transparent 3-D brain?).

Our quantitative RT-PCR data is formatted in an excel spreadsheet similar to below:
Gene 1 Gene 2 Gene 3 Gene 4
thalamus 1.001 1.113 1.234 1.034
cingulate gyrus 0.998 -0.033 1.001 1.502
sup temp lobe 1.222 1.103 0.899 0.988
med temp lobe -0.022 -0.112 -0.045 1.001

I can compile in Unix and have good Unix and Mac OSX skills and reasonable Windows skills, but absolutely no experience in 3-D modeling or OpenDX or any other kind of rendering programs. We currently present these quantitative RT-PCR data in a table or use the Excel or SPSS charting function to create a figure (though not a very inspiring figure).

I would greatly appreciate some guidance as to how to project these RT-PCR data on a 3-D representation of the brain.

Ultimately, I would like to contrast these RT-PCR data with our fMRI data that we have generated from subjects given reading tasks while in the fMRI scanner. Currently, our fMRI collaborators have supplied us with data presented in 2-dimensional brain slices. I would like to project the fMRI data and the expression data in the same graphic format to best show how they are similar and how they differ.

Any guidance in this area would be greatly appreciated.

Sincerely,

Jeff Gruen

Jeffrey R. Gruen, MD
Associate Professor of Pediatrics
Yale University School of Medicine
Yale Child Health Research Center
Email: jeffrey.gruen@yale.edu