CUMC-E interactome

A cell regulatory network for pancreatic carcinogenesis (CUMC-E interactome) was reverse-engineered by ARACNe-AP using 242 epithelial LCM-RNA-Seq gene expression profiles. Genes with detection rates at 0.1 TPM below 25% in all of the examined conditions (PanIN, IPMN, and PDA) were removed and the variance was stabilized by fitting the dispersion to a negative binomial distribution as implemented in the DESeq R package. ARACNe was run with standard settings (using data processing inequality (DPI), with 100 bootstrap iterations using human gene symbols mapping to a set of 1665 transcription factors and 1025 transcription cofactors as described from AnimalTFDB 3.0.