TABLE 4.

Gene Sets Enriched in ITE Samples (vs. DMSO)

Rank ITEa	Rank TCDDb	Gene set name	Descriptionc	# Genes in setd	FDR q valuee	Nominal p value
1	6	Dendritic cell pathway	ANPEP, several interleukins, TLRs, interferons, and CD molecules	21 (2)	0.047	0.000
2	3	Arachidonic acid metabolism	PTGS1,2; carbonyl reductases; GGT; PTGES, PTGDS; phospholipases, Cyp2U1 and 2E1; and GPXs, …	40 (10)	0.138	0.002
3	4	IDX TSA DN cluster1	Genes downregulated 48–96 h during 3T3-L1 fibroblast differentiation into adipocytes with IDX (insulin, dex, and isobutylxanthine)	40 (12)	0.094	0.000
4	25	γHexachlorocyclohexane degradation	Acid and alkaline phosphatases, Cyp3a's, and paraoxonases	14 (4)	0.118	0.000
5	2	Fatty acid metabolism	AcylCoA dehydrogenases, oxidases, synthetases; ADHs, AldHs, many P450s, …	60 (10)	0.101	0.000
6	5	Metabolism of xenobiotics by cytochrome P450, …	Many AldHs, Cyps, GSTs, epoxide hydrolase, and UDPGTs	34 (7)	0.116	0.002
7	1	Prostaglandin and leukotriene metabolism	Lipoxygenases, Cyp4F's, carbonyl reductases, PTGES, and phospholipases, …	28 (7)	0.193	0.000
8	15	Greenbaum E2A DN	E2A target genes in lymphocyte development	25 (8)	0.170	0.004
9	9	Eicosanoid synthesis	PG synthases, arachidonate lipoxygenases, PTGS1,2	16 (7)	0.153	0.004
10	10	Butanoate metabolism		27 (8)	0.231	0.006
11	43	Pomeroy desmoplasmic versus classic MD_DN	Genes expressed in classic medulloblastomas	37 (2)	0.236	0.002
12	13	Nicotinate and nicotinamide metabolism		22 (8)	0.241	0.006
13	14	Valine, leucine, and isoleucine degradation	Transferases, dehydrogenases, …	35 (10)	0.225	0.007
(6)f	(11)	TGFβ signaling pathway	TGFβs, TGFRs, LTBP1; bone morphogenic proteins, Id1–4; MAPK1,3; protein phosphatase 2’s; CDK inhibitor 2B	82 (27)	0.510	0.002

Note. Listed are the gene sets which were identified by GSEA to be enriched in ITE-treated cells compared with DMSO treated, with FDR < 25%. ADHs, alcohol dehydrogenases; AldHs, aldehyde dehydrogenases; ANPEP, alanyl aminopeptidase; GGT, g-glutamyl transpeptidase (or gamma-glutamyl transpeptidase); GPXs, glutathione peroxidases; GSTs, glutathione S-transferases; MAPK, mitogen-activated protein kinase; PG, prostaglandin; PTGS, prostaglandin endoperoxide synthase; PTGES, prostaglandin E synthase; PTGDS, prostaglandin D synthase; TLR, toll-like receptor; UDPGTs, UDP-glucuronyltransferases.

^aRank within the enriched gene sets, based on normalized enrichment score (ITE vs. DMSO). Rank differs among repeated runs of GSEA due to random permutation process of analysis.

^bRank within enriched gene sets (TCDD vs. DMSO).

^cSome of the genes/classes of genes included in indicated gene set.

^dTotal number of genes in set (number individually induced in ITE samples).

^eFDR, estimated probability that set represents a false positive.

^fOne of the sets downregulated by ITE and TCDD relative to DMSO; FDR > 25% (as it is for all downregulated sets).