Applications of a rat multiple tissue gene expression data set

Abstract

With the sequencing and assembly of the rat genome comes the difficult task of assigning functions to genes. Tissue localization of gene expression gives some information about the potential role of a gene in physiology. Various examples of the utility of multiple tissue gene expression data sets are illustrated here. First, we highlight their use in finding genes that might play an important role in a particular tissue on the basis of exclusive expression in that tissue or coexpression with a gene or genes with known function. Second, we show how this data might be used to explain known phenotypic differences between strains. Third, we show how expression patterns of genes in a genomic interval might identify candidate genes in quantitative trait loci (QTL) mapping studies. Lastly, we show how multiple tissue and species data can help researchers prioritize follow up studies to microarray experiments. All of these applications of multiple tissue gene expression data sets will play a role in functionally annotating the rat genome.

Figure 1

Catechol-O-Methyltransferase (COMT) mRNA levels are increased in Wistar Kyoto compared with Sprague Dawley frontal and cerebral cortices. Red represents expression level of a transcript that is above the median expression level across the tissues shown, whereas green represents expression below the median. The intensity of the color corresponds to the magnitude of the change.

Figure 2

A set of transcripts shows a high expression correlation to the D1 dopamine receptor across many rat tissues. Highlighted sequences had Pearson coefficients across tissues of at least 0.8. Red represents expression level of a transcript that is above the median expression level across the tissues shown, whereas green represents expression below the median. The intensity of the color corresponds to the magnitude of the change.

Figure 3

An uncharacterized transcript shows an enriched expression in all striatal (dorsal and ventral striatum, nucleus accumbens) tissues. Expression profile of this transcript, rc_AI639435_at = AI639435, is displayed using Affymetrix MAS5 signal intensity across many tissues. This sequence was found using the GROW function of the Rosetta Resolver software package (see Methods and Supplemental Table 1), and shows a highly correlated expression pattern to known striatal genes. A similar image can be obtained on http://expression.gnf.org/ratlas.

Figure 4

Corticotropin release hormone receptor 2 shows enriched expression in brain regions involved in alcohol preference, especially the nucleus accumbens core and shell, whole nucleus accumbens, and central nucleus of the amygdala. Expression profile of this transcript is displayed using Affymetrix MAS5 signal intensity across many tissues. A similar image for this sequence, U16253_at = U16253, can be found at http://expression.gnf.org/ratlas.

Figure 5

A novel transcript with differential expression in a model of cocaine craving shows a dramatically enriched expression in drug addiction-related brain regions. Expression profile of this transcript, AF055714UTR#1_at = AF055714, is displayed using Affymetrix MAS5 signal intensity across many tissues. A similar image can be obtained on http://expression.gnf.org/ratlas.