Table 2 Genes are ranked based on the mediator score from the final ranked gene list across all tumor nodules. The top 5% ranked genes are shown, excluding the ones with a FDR adjusted P-value > 0.05 after the random permutation test. For each gene, the gene name and type are given. For each tumor nodule, +1 denotes upregulation at the RNA, proteome or phosphoproteome levels. Similarly, -1 denotes downregulation. If empty, the gene’s, protein’s or phosphosite’s levels did not change significantly between tumor nodules and control samples

phosphatase

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

transcription activator

1

1

1

1

1

1

1

1

1

1

1/0

1/0

1/0

transcription factor

-1

1/0

1/0

transcription factor

kinase

-1

-1

-1

-1

1/0

kinase

-1

transcriptional regulator

kinase

1

1

1

1

1

1

1

1

1

1

1

1

transcriptional inhibitor

-1

-1

-1

-1

kinase

1

1

1

1

1

1

1

1

1

1

1

1/0

1/0

0/1

2/0

1/0

arginase

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

0/1

0/2

0/1

0/2

E3 ubiquitin protein ligase

1

1

1

1

1

1

1

1

transcription factor

1

1

1

1

1

1

1

1

1

1

1

1

deacetylase

-1

-1

-1

-1

transcription factor

-1

-1

kinase

-1

1

growth factor

-1

-1

-1

-1

-1

-1

-1

-1

growth factor

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

0/1

0/1

0/1

0/1

0/1

transcription factor

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

1

-1

1

1

1

1

1/0

1/0

1/2

3/0

3/0

3/0

2/0

kinase

-1

1

1

1

0/1

transcriptional repressor

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

deacetylase

1/0

1/0

kinase

-1

-1

methyltransferase

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1/0

transcription factor

1

1

1

1

1

1

S-transferase

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1/0

1/0

2/0

1/0

cyclin

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

chloride intracellular channel

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

kinase

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1/0

1/0

1/0

1/0

kinase

1

1

1

1

1

-1

growth factor

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

chromatin-binding factor

-1

1

0/1

0/1

transcription factor (forkhead family)

-1

-1

1/0

kinase

-1

-1

-1

1

transcription factor

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

mitochondrial uncoupling proteins

1

1

1

1

1

1

1

1

1

1

1

1

growth inhibitory protein

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

1

0/1

0/2

0/1

signal transduction proteins

1

1

1

1

inhibitor metalloproteises

1

1

1

1

1

1

1

1

1

1

1

1

aspartic proteases

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

transcription factor

adapter protein

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1/0

Insulin Receptor Substrate

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

transcription factor

1

1

1

1

1

1

1

1

1

1

1

Histone-lysine N-methyltransferase

1

1

lymphoid-specific helicase

1

1

1

1

1

1

1

1

1

1

1

1

-1

anti- and pro-apoptotic regulators

-1

kinase

versican proteoglycan

1

1

1

1

1

1

1

1

1

1

1

1

transcription factor

-1

-1

-1

-1

-1

-1

-1

-1

1/0

spermidine Synthase

1

1

1

1

1

1

enzyme in polyamine biosynthesis

1

1

1

1

1

1

1

1

1

1

1

1

inhibits axol extension

transcription factor

-1

-1

0/1

transcription activator

1

1

1

1

1

1

1

1

1

1

1

1

secreted mitoattractant

1

1

1

1

1

1

1

1

1

1

1

1

Ras protein

1

1

1

transcription factor

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

1

kinase

1

1/0

1/0

1/0

1/0

1/0

1/0

transcriptional regulator

chromosomal protein

-1

-1

-1

-1

-1

-1

-1

1

-1

0/1

0/2

1/0

phosphatase

phosphatase

1

1

1

1

1

1

1

1

1

1

1

1

1

1/0

1/0

transcription factor

1

acetylhydrolase

1

1

1

kinase

-1

-1

1

1

1

1

1

1

1

1/0

1/1

1/0

0/1

vitamin D receptors

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

calcium binding protein

1

1

1

1

1

1

1

transcription factor

transcriptional modulator

-1

-1

-1

-1

-1

-1

Ras protein

1

1

1

1

1

1

1

1

1

1

1

1

transcription factor

-1

-1

-1

-1

-1

-1

-1

-1

-1

-1

kinase

1

1

1

1

-1

1

1

1

1

1

1

2/0

1/0

1/0

2/0

3/0

scaffolding protein within caveolar membranes

1

1

1

1

1

1

1

1