Table 1 Overview over gene-signature quantification methods.
Method | Description | Method class |
---|---|---|
cor_p_AC | Pearson correlation of the compound signature to the active control signature | direction |
cor_s_AC | Spearman rank correlation of the compound signature to the active control signature | direction |
cos_AC | Cosine of the compound signature to the active control signature | direction |
cos_weight_AC | cos_AC * significance_weight. Idea: downweight cosine values for signatures with very small / non-significant amplitudes, likely caused by noise. Significance weight = weight from 0 to 1 quantifying the significance of the signal amplitude of the compound gene-signature vector. Formula: min(1, mean(abs(gene rscores)) /3). The mean of the absolute gene expression value rscores of the signature readouts divided by 3 equals 1, if on average the rscores of the signature are 3 standard deviations away from the background. This is considered the threshold from where on signals are considered strong enough not to be downweighted. This score requires the gene expression readouts to be scaled as rscores. Rscores give the number of robust standard deviations where a gene expression of a treatment is away from the median of untreated NC conditions (rscoreā=ā(fold change treatment ā median fold change NC) / mad (NC)) | direction |
dot_p_AC | Dot product of compound signature with the active control signature | direction&magnitude |
scalar_projection_AC | Scalar projection of the signature to the active control signature | direction&magnitude |
vec_norm | Norm of the compound signature vector | magnitude |
euc_NC | Euclidean distance of compound signature from neutral control signature | magnitude |
maha_NC | Mahalanobis distance of the compound signature from the neutral control signature | magnitude |
num_readouts_changed | Number of readouts with signal different from background (abs(rscore of gene)> 3) | magnitude |
euc_AC | Euclidean distance of the compound signature to the active control signature | AC_similarity |
maha_AC | Mahalanobis distance of the compounds signature to the active control signature | AC_similarity |