Table 2. Numbers of (A) significantly up- and downregulated genes and gene sets and (B) significantly activated and inhibited pathways.

A)				Significant genes		Significant gene sets1 (qusage)
Test	Sample subset	FDR	Direction	Protein coding	Non-coding	C1	C2	C3	C4	C5	C6	C7
Miliary vs non-miliary	All	10%	Up	33	8	43	269	7	89	104	2	19
			Down	32	17	101	2 150	404	315	699	117	1 046
Miliary vs non-miliary	A,S	10%	Up	59	18	1	3	0	1	2	1	2
			Down	110	28	0	12	0	1	5	0	1
Miliary vs non-miliary	P,M	10%	Up	2	0	67	499	20	131	164	5	37
			Down	0	0	106	2 451	365	425	813	114	1 370
AS vs PM	Non-miliary	5%	Up	641	222	3	389	11	80	63	1	423
			Down	510	164	5	246	49	24	63	4	19
AS vs PM	Miliary	5%	Up	94	28	1	132	8	52	23	0	146
			Down	296	179	4	267	84	11	34	6	39
From total:				16 674	11 529	326	4 722	836	858	1 454	189	1 910

B)		SPIA				PAGI
Test	Sample subset	FDR	Direction	Pathways (Supp. Figure)	Number of used genes	FDR	Pathways
Miliary vs non-miliary	All	10%	Activated	0	845	n.d.
			Inhibited	3 (S6)	(FDR 20%)
Miliary vs non-miliary	A,S	10%	Activated	5 (S7)	215	1%	76
			Inhibited	6 (S7)
Miliary vs non-miliary	P,M		Activated	n.d.2	(2)	1%	11
			Inhibited	n.d.
AS vs PM	Non-miliary	5%	Activated	16 (S8)	1 537	n.d.
			Inhibited	7 (S8)
AS vs PM	Miliary	5%	Activated	8 (S9)	597	n.d.
			Inhibited	0
		From total:	156			219

¹C1, positional gene sets; C2, curated gene sets; C3, motif gene sets; C4, computational gene sets; C5, GO gene sets; C6, oncogenic signatures; C7, immunologic signatures.

²n.d., not determined.