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Help: Normalized Gene Expression
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Description
Normalized gene expression presents the relative expression level of a gene (defined as a UniGene Cluster) in different tissues and is "normalized" for the number of clones from each tissue that are included in UniGene.
Description of the Calculation
A UniGene cluster's expression in tissue types is approximated as follows:Clones are first sorted by tissue; all clones from libraries that UniGene reports as derived from the same tissue are treated as having come from the same tissue, even thought they may have come from different libraries. No attempt is made to relate the different libraries by anything other than the tissue name reported in UniGene, so "cerebellum" and "brain" will be listed separately, even though the cerebellum is part of the brain.
The approximate frequency of a UniGene cluster's occurrence within each tissue is then calculated:
| A = B / C
|
| Where A = Frequency of the UniGene cluster's expression within the tissue, B = Number of UniGene clustered clones within the tissue and, C = Total number of unique clones from the same tissue in the UniGene database |
The frequencies within each tissue are summed to find the total expression within UniGene.
| D = A1 + A2 + A3 + ... |
| Where D = Summation of UniGene Cluster Expression Frequencies, by Tissue, A1 = Freq. of UniGene cluster expression in tissue 1, A2 = Freq. of UniGene cluster expression in tissue 2, and A3 = Freq. of UniGene cluster expression in tissue 3, etc. |
Normalized UniGene cluster expression within a tissue is then calculated by dividing the frequency of the UniGene cluster's occurrence in a tissue by the summation of UniGene cluster expression frequencies, by tissue.
| normalized gene expression within a tissue = A / D
|
| Where A = Frequency of the UniGene cluster's expression within the tissue, and D = Summation of UniGene Cluster Expression Frequencies, by Tissue |
Hypothetical Calculation
Clones for a gene identified by UniGene Cluster X have been isolated from skeletal muscle (9 unique clones) and cardiac muscle (1 unique clone). For each tissue, the approximate frequency of the cluster's occurrence is calculated:
| Frequency of | 9 (Number of skeletal muscle clones in UniGene Cluster X) | ||
| UniGene Cluster | = | = 0.000600 | |
| in skeletal muscle | 15000 (Total number of clones from skeletal muscle in UniGene) |
| Frequency of | 1 (Number of cardiac muscle clones in UniGene Cluster X) | ||
| UniGene Cluster | = | = 0.000100 | |
| in cardiac muscle | 10000 (Total number of clones from cardiac muscle in UniGene) |
| Summation of UniGene Cluster Expression Frequencies, by Tissue = 0.000600 + 0.000100 = 0.000700 |
Normalized gene expression is then calculated by dividing the frequency of the cluster's occurrence in a tissue by the summation of UniGene cluster expression frequencies.
| normalized expression of Unigene Cluster X in skeletal muscle = 0.000600 / 0.000700 = 85.71% in skeletal muscle |
| normalized expression of Unigene Cluster X in cardiac muscle = 0.000100 / 0.000700 = 14.29% in cardiac muscle |