Table 1.

Scores assigned by the profile search and binding of RFX and CIITA to S-Y modules

S-Y modulea	Score	Binding of RFX (ChIP)b	Binding of CIITA (ChIP)b	Binding of CIITA in B cells (ChIP-on-chip)c	Binding of CIITA in DC (ChIP-on-chip)c	Binding of CIITA in B cells (ChIP-on-chip HD)c,d
DRB5	20.79	—e	—	59	40	57
DRB1	18.73	—	—	81	45	57
DRA	18.15	100	100	100	100	100
DRAe	17.91	50	30	47	61	38
DQB	17.44	—	—	34	11	41
RAB4B	17.33	47	22	48	52	69
DPA	17.27	103	79	29	62	19
#4	17.02	59	49	28	31	33
Ii	15.02	41	33	32	33	54
DOB	14.65	—	4	44	27	79
DMA	14.63	—	—	61	49	62
DPB	14.07	41	13	28	80	40
DOA	13.57	—	15	30	19	29
#8	13.24	103	108	—	—	27
DMB	13.02	14	7	43	40	46
#2	12.59	93	92	—	—	47
Ii S′-Y′	12.45	80	19	—	—	28
DQA	11.18	—	3	19	18	1
Ii Y′′-S′′	10.42	19	6	—	—	33
#6	9.33	52	16	—	—	42

^aS-Y modules found in the promoter-proximal regions of the indicated MHC-II genes, or in distal enhancers (DRAe, Ii S′-Y′, Ii Y′′-S′′, #2, #4, #6 and #8) described previously (20,30).

^bin B cells, relative to DRA (set at 100%).

^cvalues were calculated as peak surfaces (peak length multiplied by the average intensity obtained for separate probes) and represented relative to DRA (set at 100%).

^dHD, high density array.

^e—, not done (ChIP) or not on array (ChIP-on-chip).