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High expression is defined as an expression value that is one Median Absolute Deviation or more than the median expression for that particular tissue.
The tissue-related gene expression resource Symatlas was searched for genes expressed in either fetal liver or placenta, at a level that is a (user-definable) multiple of the median expression for that gene across all tissues.
Median expression for each cluster was calculated.
†high ESR1 = above median expression for Luminal A; low ESR1 = below median expression for HER2-enriched.
‡high PGR = above median expression for Luminal A; low PGR = below median expression for Luminal B. §high ERBB2 = above median expression for HER2-enriched; low ERBB2 = below lowest quartile expression for HER2-enriched.
Inputs to the algorithm were the logged median expression for each gene and the parameters, c and m, discussed above.
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Expression data was clustered into 6 groups using the SOM and displayed as a plot of the normalized median expressions for each protein with respect to its group values.
T X) represents the set of tissues in which X is expressed above median expression value for that tissue.
Raw data was transformed by taking the median expression value for the patient data for each protein within each group.
The median expression levels for all proteins investigated were calculated for hormone-sensitive and -refractory tumours (Table 1).
To find a representative HIV-related module under a specific stage, thus, we used a median value of multiple co-expression scores for an interaction and a median expression level for a protein, respectively.
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