Table II. Summary of gene expression in IBD along with functions and transcriptional regulation.

Genes were quantified in this study with real time RT-PCR using FFPE colon biopsy samples from active UC (aUC), active CD (aCD), quiescent/ histologically normal-appearing colon from UC (qUC), and quiescent CD (qCD).

Category	Transcription Regulation	Function	Gene	Active UC	Quiescent UC	Active CD	Quiescent CD
Cytokines	TLR/NFκB	+NF-κB/Apoptosis	TNF-α	++	NC	++	NC/+
	NF-kB/AP1	+Neutroph/CXCR1/2	IL-8	+++	NC	+++	NC
	NF-κB/STAT3	+NF-κB	IL-17	+++++	NC	++++	NC
	* NF-kB	+STAT3,gp130, RAS	IL-6	+++	NC	++++	NC
	* TLRs, STAT1,IRF	+STAT4,Th1/Th17	IL-12/23 p40	+	NC	+++	NC
	* STAT4	+STAT1/STAT2	IFN-γ	NC/+	NC	++	NC/+
	Sp1/3, Antigen	+STAT6/PI3K	IL-13	+++	+	NC	NC
	TRAF6/NF-κB/AP1	+NF-κB/st2/MAPK	IL-33	++	+	+	NC
	* Multiple1	+STAT3, +Treg	IL-10	+++	NC	NC/+	NC
	Activation/Secretion	+SMADs, +Treg	TGF-β1	+	NC	NC/+	NC
Transcription Factors	STAT1/NFκB	+IFNγ, Th1	IRF-1	NC	NC	+++	NC
	STAT4/STAT1	+Th1 Phenotype	T-bet	NC	NC	+	NC
	STAT6	+Th2 Phenotype	GATA3	+	NC	↓	NC
	* NA	Multiple	STAT3	NC	NC	↓	NC
	SMAD1-7/STAT5	+Tregs	FOXp3	NC/+	↓	NC/+	NC
Regulators of Signaling	* NA	Kinase+ STAT1/3/4/6	JAK2	NC	NC	NC	NC
	STAT3/STAT1	(-) JAK1/2/3, STAT1	SOCS1	NC/+	NC	++	NC
	STAT3/STAT1	(-) JAK2/STAT3	SOCS3	+++	NC	+	NC
	* NFκB	(-)STAT1,ERK,p38	PTPN2	NC/+	NC	NC/+	NC
	Methylation, STATs	(-) STAT1/3/6/NF-kB	SHP-1	↓	↓	↓	NC
	NA	(-) STAT1/3,+ STAT5	SHP-2	NC	NC	NC	NC
Chemokines	* NFκB	+ MΦs/CCR2	MCP-1	+++	NC/+	+++	NC/+
	MΦ activation	MCP-1 Receptor	CCR2	++	NC	+++	NC
	* NFκB	T-cells /MΦ/CCR6	CCL20	+++	NC	++	NC/+
	* DC & T-cells	CCL20 Receptor	CCR6	+	NC	↓	NC
	IRF1/STAT1/NFκB	+Th1/CXCR10	IP-10	++	NC	+++	++
	STAT6/ NFκB	+Th2/CCR4	TARC	+++	NC	NC	NC
	STAT6/NF-κB	Monocyte/Eos/CCR3	Eotaxin 1	++	+++	NC	NC
Adhesion Molecules	STAT1/NF-κB/AP1	Binds Integ β2/LFA-1	ICAM-1	NC/+	NC	++	NC/+
	STAT6/ NF-κB	Binds Integ β1/VLA-4	VCAM-1	++	+	NC/+	NC
Oxidative Stress Inducers	* NF-κB	+PGH2/TXA2	COX2	++++	NC	++++	NC
	STAT1/NF-κB, Rac	+H2O2	Nox2	+	NC	++	NC/+
	STAT1/NF-κB	NO production	iNOS	+	NC	++	NC/+
	STAT6	Polyamine+, -Arg	Arginase1	+	NC	↓	NC
Proteases	STAT1/NF-κB	IL-1b procession	Caspase 1	NC/+	NC	+	NC
	NF-κB/APC	Mucosal degradation	MMP3	++++	NC	+++	NC
	STAT6/NF-κB	Mucosal degradation	ADAM8	+	NC/↓	NC	NC
Mucosal Defense	STAT3/Sp1	Mucus barrier	Mucin1	NC/+	NC	NC	++
	NF-κB /SP1	Mucus barrier	Mucin5aC	+++++	NC	++	NC/+
	-NF-κB/CEBPβ	Repair/anti-apoptotic	TTF3	↓	NC	NC	NC
	NF-κB	Anti-microbial	Defensin β2	++	NC	NC/+	++
	NF-κB	anti-apoptosis	BCL2	+	NC	NC/+	NC
Control	None	GAPDH, β-Actin, S18 rRNA		NC	NC	NC	NC

Expression differences are shown in relation to colon biopsies from normal subjects and an arbitrary scale was set to represent those differences: NC = no change, NC/+ = notable change that did not reach statistical significance, + = significant change under 5-fold, ++ = 5-20 fold change, +++ = 20-100 fold change, ++++ = 100-1000-fold change, +++++ = more than 1000-fold change.

^*Designates that there is documented genetic association of the genes with IBD. The transcriptional regulation of genes is described here showing transcption factors that have been documented to modulate specific gene expression and is based on reference in the text. Also the function of each gene is briefly noted. Furthermore, other genes that have been quantified and did not show significant differences include: TLR4*, CARD 9*, IFN-γ receptor 1, IL-4Rα, IL-12rb, IL-17Ar, CCR4, CCR8, CXCR3, STAT1, STAT4, STAT6*, JAK1, JAK2*, JAK3, PTPN22*.

¹Antigen stimulation of TCR, GATAT3, NFAT, AP-1, chromatin remodeling (32).