RACER fits the mRNA expression as response using as explanatory variables the TF binding signals (TFBS) from ENCODE, CNV, DM, miRNA expression signals from TCGA. Briefly, RACER infers the sample-specific TF/miRNA regulator activities, which are then used as inputs to infer specific TF/miRNA-gene interactions. The two-stage regression circumvents the problem with integrating the non-sample-specific ENCODE TFBS with the sample-specific TCGA measurements.
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Li Y, Liang M, Zhang Z (2014)
Regression Analysis of Combined Gene Expression Regulation in Acute Myeloid Leukemia.
PLoS Comput Biol 10(10): e1003908. doi:10.1371/journal.pcbi.1003908