Table 3.

Major hubs (>20 edges) in the protein interaction network of SAHA dose-responsive genes combined with transcription factors predicted to bind in the promoters of SAHA modulated genes.

Protein Hub	# Edges	Function	Response to SAHA
c-Myc	294	Transcription Factor	Downregulated
SP1*	156	Transcription Factor	N/A**
p300	94	Histone Acetyl Transferase	Downregulated
C/EBPbeta	63	Transcription Factor	Downregulated
EZH2	60	Histone Methyl Transferase	Upregulated
STAT1	53	Transcription Factor	Upregulated
CBP	49	Generic Enzyme	Downregulated
p21	48	Binding Protein	Upregulated
SP3	44	Transcription Factor	Downregulated
ETS1*	42	Transcription Factor	Downregulated
AML1 (RUNX1) *	41	Transcription Factor	Downregulated
CDK2	40	Protein Kinase	Downregulated
SMAD3	35	Transcription Factor	Upregulated
TAL1*	35	Transcription Factor	N/A**
Lck	33	Protein Kinase	Downregulated
MYOD*	32	Transcription Factor	N/A**
Bcl-2	30	Binding Protein	Downregulated
ZAP70	30	Protein Kinase	Downregulated
Caspase-1	28	Protease	Downregulated
STAT6*	28	Transcription Factor	Downregulated
HDAC3	27	Histone Deacetylase	Upregulated
ATM	26	Protein Kinase	Downregulated
SHP-1	23	Protein Phosphatase	Downregulated
Lef-1	22	Transcription Factor	Downregulated
E2F3	21	Transcription Factor	Downregulated

^*Predicted transcription factors (DiRE, http://dire.dcode.org)

^**Expression not modulated by SAHA