This column shows the gene expression data from the Mouse Gene Expression Atlas 2 from the Genomics Institute of the Novartis Research Foundation (GNF).
By default, the column shows the ratio of expression of a gene in a specific set of tissues to the expression of the gene overall. A gene that is more highly expressed in a tissue is colored red, and a less expressed gene is shown in green. The values are colored on a logarithmic scale. This coloring is standard, but is the opposite of what an inexperienced user might expect: in this case, red means go and green means stop! Black indicates that a gene is neither over- nor under-expressed in the tissue. Uncolored boxes (white on most browsers) represent missing data.
The Adult mouse tissues (10-12 weeks) were generated from two groups of 4 male and 3 female mice by dissection. For detailed information about the experiments, see Su A.I. et al. A gene atlas of the mouse and human protein-encoding transcriptomes. PNAS. 2004 Apr 20;101(16):6062-7.
When calculating expression ratios, the overall expression level in the denominator was calculated by first taking the median of replicates for each tissue, and then taking the median of these medians.
To associate particular genes with expression data we use a fairly simple-minded scheme. First we align the cDNA sequences around which the probes were designed to the genome. Then for each gene we pick the cDNA sequence with the alignment that most overlaps the gene as the source for expression data for that gene. Since many of the cDNA sequences and probes designed for the cDNA sequences just cover part of the gene, in most cases different splice varients of a gene will end up mapped to the same cDNA sequence.