This column shows microarray gene expression data from the Gladstone Institute.
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.
Several column configuration options are available on the Configuration page, which can be accessed via the configure button in the top menu.
For detailed information about the experiments, see Abeyta MJ et al. Unique gene expression signatures of independently-derived human embryonic stem cell lines. Hum. Mol. Gen. 2004 Mar 15;13(6):601-8.
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, a fairly simple-minded scheme was used. First, the cDNA sequences around which the probes were designed were aligned to the genome. Then, for each gene, the cDNA sequence with the alignment that most overlaps the gene was selected as the source for expression data for that gene. Because many of the cDNA sequences and probes designed for the cDNA sequences cover only part of the gene, in most cases different splice varients of a gene will end up mapped to the same cDNA sequence.
The data for this column were kindly provided by the Bruce Conklin lab at the Gladstone Institute at UCSF.