Table 2.

Identification of transcription factor (TF) binding sites in reovirus-induced genes in the brains of mice at early times post intracerebral inoculation (Opossum analysis)^a

TF	Bkgd gene hitsb	Bkgd gene non-hitsb	Target gene hitsb	Target gene non-hitsb	Bkgd TFBS hitsc	Bkgd TFBS rated	Target TFBS hitsc	Target TFBS rated	Z scoree	Fisher scoref
IRF2	643	14507	4	48	709	0.0006	6	0.0027	18.03	1.8e-01
STAT1	2165	12985	9	43	2693	0.0016	12	0.0042	12.52	3.2e-01
RXRA-VDR	406	14744	2	50	420	0.0003	3	0.0011	10.09	4.1e-01
IRF1	4631	10519	15	37	7857	0.0041	24	0.0071	9.566	6.6e-01

^aProbe sets that were identified as being differentially regulated (FDR < 0.1, P < .002) in T3D compared to mock-infected animals (Table 1) were analyzed for the presence of transcription factor binding sites (Opossum analysis).

^bBackground (Bkgd) genes (15,150 mouse genes were used as background/control genes). Target genes (52 reovirus-induced genes were used as target/experimental genes). Gene hits/non-hits (the number of genes, target or background, for which a TFBS was/was not predicted within the conserved noncoding regions.

^cTFBS hits. The number of times a TFBS was detected within the conserved noncoding gene regions (background or target).

^dTFBS rate. The rate of occurrence of a TFBS within the conserved noncoding regions of the genes (target or background). The rate is equal to the number of times the site was predicted (hits) multiplied by the width of the TFBS profile, divided by the total number of nucleotides in the conserved noncoding regions of the gene set.

^eZ score. The likelihood that the number of TFBS nucleotides detected for the included target genes is significant as compared with the number of TFBS nucleotides detected for the background set. Z score is expressed in units of magnitude of the standard deviation. A Z score of > 10 was used as an indication of significance based on empirical studies (Opossum software).

^fFisher score. The probability that the number of hits versus non-hits for the included target genes could have occurred by random chance based on the hits versus non-hits for the background set. A Fisher score of < .01 was used as an indication of significance based on empirical studies (Opossum software).

IRF2 = interferon regulatory factor 2; IRF1 = interferon regulatory factor 1; RXRA = retinoid × receptor alpha; VDR = vitamin D receptor; Bkgd = background; TF = transcription factor; TFBS = transcription factor binding site; STAT1 = signal transducer and activator of transcription 1.