As input for our algorithm, we used a dataset composed of expression data measured on 89 tumor and normal tissue samples (representing 11 tumor classes) both for 11,833 messenger RNAs and 124 miRNAs [13].
B. mori microarray database is composed of expression data for 22987 probes of 9 silkworm tissues on day 3 of the fifth instar in silkworm [ 25].
Therefore, while both SAM and PIR identified the same sub-set of transcripts within compound, the PIR method detected a larger component of the global transcriptional response of the cortex composed of expression changes that do not fit a linear model.
The method is based on an analysis of the intensity distribution of all microarray probe sets mapped to a three dimensional feature space composed of average expression level, average difference of gene expression and total variance.
The data set was composed of mRNA expression data for 164 distinct small molecules and corresponding vehicle controls applied to human cell lines (564 gene expression profiles in total, representing 453 individual instances).
This dataset is composed of the expression of 2,467 genes on 79 samples corresponding to 8 different experiments of the budding yeast: alpha factor (18 samples), cdc15 (15 samples), cold shock (4 samples), diauxic shift (7 samples), DTT shock (4 samples), elutriation (14 samples), heat shock (6 samples) and sporulation (11 samples).
The second cluster is composed of gene expression (mRNA levels of ef1, igf1, igf1r, ghr, and β-actin ; Figure 1).
These are composed of the expression profile, x exp = (e1, e2,..., e N ) and the sequence profile, x seq = (m1, m2,..., m M ) of each gene.
Validation set 2, from Lee et al. [ 10], is composed of gene expression and clinical information from 191 GBM patients (GEO accession [GSE13041]).
Validation set 4, from Phillips et al. [ 9] and Costa et al. [ 20], is composed of gene expression and clinical information from 77 GBM patients (GEO accession [GSE4271]).
Validation set 1, from Freije et al. [ 7], is composed of gene expression and clinical information from 74 GBM patients (GEO accession [GSE4412]).
