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.

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Correction statement     Genes no longer variable In the re-analysis of Project Normal, these genes no longer showed statistically significant mouse variance.   No longer variable - Download Tab Delimited No longer variable as tab delimited files - right click and use save link as to download           Testis       Liver       Kidney     Significantly Variable Genes This list of genes has been corrected in the reanalysis of the Project Normal dataset   Significantly Variable Genes - Download Reanalyzed Significant variable genes as tab delmited files - right click and use save link as to download.         Testis       Liver       Kidney     Scaled Complete Analysis 'Scaled' spread sheets included scale adjusting for the normalization of the array data. What this means is that median of the deviation from the median was set to the same value for the distribution of all the log-ratios on each array. This is the form of normalization that was used for the paper.   Complete analysis of variable genes - Download Tab delimited Full scaled complete analysis as tab delimited files - right click and use save link as to download       Testis Scaled       Liver Scaled       Kidney Scaled     Raw Data Sets The notation in the raw 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     Raw Data - Download Tab delimited Raw Data sets as tab delimited files - right click and use save link as to download         Testis       Liver       Kidney     TIF Image Files Raw Images of the arrays in TIF format       Testis       Liver       Kidney     Mouse Merge File Merge file for the mouse array     Merge File   Merge File - Updated 06/22/2003 - Includes chromosome     Data made available with permission from Colin C. Pritchard and Peter S. Nelson.