Table 3.

Up-regulation of immune response genes in skeletal muscles of patients with active JDM longer than 2 months (Cluster C and D; genes are in order shown in figure 1)

Affymetrix accession	p-value	Fold change (long/short)	Gene description
Cluster C
203981_s_at	6.2E-03	1.5	ATP-binding cassette, sub-family D (ALD), member 4
210105_s_at	1.5E-03	1.6	FYN oncogene related to SRC, FGR, YES
214430_at	1.4E-03	1.6	galactosidase, alpha
200602_at	6.5E-04	2.0	amyloid beta (A4) precursor protein
201103_x_at	5.7E-03	1.4	hypothetical protein LOC200030
209765_at	2.3E-03	1.6	a disintegrin and metalloproteinase domain 19
216510_x_at	9.6E-04	5.6	immunoglobulin heavy constant gamma 1
201069_at	3.9E-03	2.0	matrix metalloproteinase 2
203473_at	1.1E-04	2.2	solute carrier organic anion transporter family, member 2B1
203742_s_at	1.9E-03	1.5	thymine-DNA glycosylase
205917_at	6.5E-04	1.6	ZNF264
212671_s_at	2.5E-04	5.6	major histocompatibility complex, class II, DQ alpha 1/2
Cluster D
218376_s_at	4.1E-03	2.5	NEDD9 interacting protein with calponin homology and LIM domains
209079_x_at	9.1E-04	1.6	protocadherin gamma subfamily
38671_at	5.9E-04	1.6	plexin D1
201279_s_at	2.0E-03	1.6	disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)
211066_x_at	6.5E-04	1.6	protocadherin gamma subfamily
215599_at	3.8E-04	2.1	SMA4
205717_x_at	1.8E-03	1.4	protocadherin gamma subfamily
217659_at	1.3E-03	1.6	KIAA0261
212607_at	1.1E-04	1.3	AKT3 (protein kinase B, gamma)
211748_x_at	4.0E-03	2.4	prostaglandin D2 synthase 21 kDa (brain)
215376_at	2.4E-04	1.4	CDNA FLJ12295 fis, clone MAMMA1001818
202259_s_at	1.1E-04	1.6	phosphonoformate immuno-associated protein 5
212187_x_at	2.1E-03	1.9	prostaglandin D2 synthase 21 kDa (brain)
206666_at	3.7E-04	2.5	granzyme K (serine protease, granzyme 3; tryptase II)
217947_at	5.9E-04	1.9	chemokine-like factor super family 6