For comparisons of primary tumors and metastases [ 32, 33], we used the normalized expression matrices as input for GSEA to test if functional groups were differentially expressed between metastases and primary tumors.
b Read alignments, quality control (QC), and specific processing steps create "feature expression" matrices, where cells are represented as vectors and genomic features (e.g. gene expression, methylation) represented as columns.
To simulate expression matrices, we assumed two different models: 1. Coherent model.
Generation of expression matrices, data annotation, filtering and processing have been previously described [19].
Although seriesMatrix files should ideally contain log-transformed data, expression matrices in linear scale were also observed in several cases.
The differences between both approaches can also be seen by visualizing the ordered expression matrices (data not shown).
No filtering means using the complete gene expression matrices with all the human gene probesets present in the microarrays.
Given two genes in one of our expression matrices we used different quantitative measures of coexpression to construct independent sets of RCGs.
Generation of expression matrices, data annotation, filtering and processing were performed as described previously using the TableButler software package (http://www.OncoExpress.org/software/tablebutler) [25], [26].
The Iterative Signature Algorithm is an iterative extension of the Signature Algorithm, designed for a global decomposition of large-scale expression matrices into transcription modules, in the absence of a-priory information.
Upload miRNAs and genes expression matrices.
