Published in November 6, 2001 volume 98:23 of PNAS on pages 13266-13271
Project normal: Defining normal variance in mouse gene expression
Colin C. Pritchard, Li Hsu, Jeffrey Delrow, and Peter S. Nelson
|  | The mouse has become an indispensable and versatile model organism for the study of development, genetics, behavior, and disease. The application of comprehensive gene expression profiling technologies to compare normal and diseased tissues or to assess molecular alterations resulting from various experimental interventions has the potential to provide highly detailed qualitative and quantitative descriptions of these processes. Ideally, to interpret experimental data, the magnitude and diversity of gene expression for the system under study should be well characterized, yet little is known about the normal variation of mouse gene expression in vivo. To assess natural differences in murine gene expression, we used a 5406-clone spotted cDNA microarray to quantitate transcript levels in the kidney, liver, and testis from each of 6 normal male C57BL6 mice. We used ANOVA to compare the variance across the six mice to the variance among four replicate experiments performed for each mouse tissue. For the 6 kidney samples, 102 of 3,088 genes (3.3%) exhibited a statistically significant mouse variance at a level of 0.05. In the testis, 62 of 3,252 genes (1.9%) showed statistically significant variance, and in the liver, there were 21 of 2,514 (0.8%) genes with significantly variable expression. Immune-modulated, stress-induced, and hormonally regulated genes were highly represented among the transcripts that were most variable. The expression levels of several genes varied significantly in more than one tissue. These studies help to define the baseline level of variability in mouse gene expression and emphasize the importance of replicate microarray experiments.

See the technical paper
See the supporting figures
Additional Significantly variable genes

- Testis
- Liver
- Kidney

Full Data Sets
Full Data sets as tab delimited files - right click and use save link as to download

The notation in the full files is as follows:
M1 | Mouse number
K, T, L | K = Kidney, T = Testis, L = Liver
3, 5 | Cy dye that contains experimental channel data
_1, _2, _3 | Replicate number for that mouse/tissue/cy dye combination

- Testis
- Liver
- Kidney

Hint: F635, B635, F532, and B532 stand for foreground and background of singal intensity at wavelength 635 and 532, respectively

Images
Listings of TIF images

The notation in the full files is as follows:
M1 | Mouse number
K, T, L | K = Kidney, T = Testis, L = Liver
3, 5 | Cy dye that contains experimental channel data
_1, _2, _3 | Replicate number for that mouse/tissue/cy dye combination

- Testis - Testis Ratio
- Liver - Liver Ratio
- Kidney - Kidney Ratio

Hint: images are viewable with Adobe Photoshop 5.5 but do not appear to be viewable with standard Windows 2000/XP tools

Data made available with permission from Colin C. Pritchard and Peter S. Nelson.