Table 3.

Classification of the up- and down-regulated genes in all MG subgroups^a

Biological Process		Fold Change
Molecular function	GenBank	MH	ML	SN	Name
Up-regulated genes
Immune response (19)
B cell related	BG759817	3.38	2.20	2.64	CD79A Ag
B cell related	BG024663	2.71	2.04	2.37	CD20 Ag
B cell related	M84371	2.63	1.99	1.88	CD19 Ag
B cell related	M27394	1.98	2.23	2.18	CD20 Ag
Chemokine	AF044197	2.82	1.97	1.95	CXCL13
Complement component	K02765	2.94	2.16	2.05	Complement component 3
IFN-induced	AF024714	2.09	2.44	1.99	IFN-inducible protein (AIM2)
IFN-induced	X82200	2.06	2.11	2.26	Staf50
Ig family	AI634950	5.06	2.09	2.76	Ig H constant μ
Ig family	BM008087	3.42	2.53	3.84	Ig H constant μ
Ig family	Z98733	2.80	2.79	2.55	Ig H chain variable region
Ig family	M63438	2.63	3.43	2.11	Ig κ chain variable region (IGKV gene)
Ig family	Z46347	2.56	1.97	2.02	Ig κ chain V-IV region B17 precursor
Ig family	Y14738	2.32	2.46	2.33	Ig λ L chain
Ig family	M63438	2.17	2.99	2.29	Ig κ chain variable region (IGKV gene)
Ig family	D87023	2.09	2.65	2.09	Ig λ
MHC class II	BF795929	2.47	2.27	2.85	MHC class II, DR α
MHC class II	BG619272	2.31	2.72	2.98	MHC class II, DQ β 1
MHC class II	M24364	2.13	1.97	1.89	MHC class II, DQ β 1
Transcription (11)
Transcription factor activity	BG760057	3.72	2.38	2.14	T-cell leukemia/lymphoma 1A
Transcription factor activity	AV747778	4.15	4.20	2.48	v-fos FBJ murine osteosarcoma viral oncogene homolog
Transcription factor activity	NM_003451	3.63	3.45	3.70	Zinc finger protein 177
Transcription factor activity	D31716	3.56	4.03	2.46	Basic transcription element-binding protein 1
Transcription factor activity	U20734	2.94	2.26	2.16	Transcription factor junB (junB)
Transcription factor activity	M92844	2.41	3.06	2.25	Zinc finger transcriptional regulator (GOS24)
Transcription factor activity	AL549846	2.07	1.95	2.16	TGF β-induced factor
Transcription factor activity	X63741	1.80	2.04	1.85	Early growth response 3
Transcriptional regulation	BF305705	2.07	2.51	2.43	Histone deacetylase 5
Transcriptional regulation	R56503	1.94	2.06	2.01	SWI/SNF-related protein, subfamily a, member 2
Transcriptional regulation	U66615	1.89	2.07	2.28	SWI/SNF-related protein, subfamily c, member 1
Cellular/intracellular signaling (5)
Calcium-binding protein	AV713821	2.64	1.92	2.22	S100 calcium-binding protein A4
Calcium-binding protein	BC009846	1.96	2.32	2.10	Hippocalcin-like 1
Cell adhesion	AU124258	1.89	2.07	2.06	Desmoglein 2
Channel	U72245	1.80	1.96	1.91	Phospholemman chloride channel
Receptor activity	BG325212	2.67	2.11	2.08	IGF-2 receptor
Cellular metabolism (4)
Nucleotide metabolism	AL535356	2.97	2.27	2.70	Ribosomal protein S7
Nucleotide metabolism	BI259616	2.73	3.19	1.99	Uracil-DNA glycosylase 2
Nucleotide metabolism	BG252637	1.96	2.56	3.03	Prostatic binding protein
Protease	AL541945	2.15	2.39	2.57	Serine proteinase inhibitor, clade F, member 1
Divers (3)
Unknown		2.18	2.11	2.11	Incyte EST
Unknown	Z69892	2.02	1.85	2.16	Clone ICRFp507I1077
Unknown	AL050127	1.93	2.17	2.22	Clone DKFZp586G021
Down-regulated genes
Cellular metabolism (13)
ATP binding activity	D29641	−2.17	−1.93	−2.12	Helicase SKI2W
ATP binding activity	U56602	−2.28	−2.43	−2.21	Peroxisomal biogenesis factor 6
ATP biosynthesis	D50371	−2.19	−2.16	−1.94	ATP synthase subunit e
Cell cycle	D86958	−1.87	−1.94	−1.95	RB1-inducible coiled-coil 1
Protein processing	AF110647	−1.93	−2.12	−2.05	Translocon-associated protein γ subunit
Protein processing	BC001687	−2.05	−2.21	−1.91	Asparaginyl-tRNA synthetase
Protein processing	BF796127	−4.74	−4.34	−3.71	Vacuolar protein sorting 45B
Ribosome biogenesis	AL526336	−2.14	−2.42	−1.97	EBNA1-binding protein 2
RNA binding	BE501622	−2.20	−2.29	−1.85	Small nuclear ribonucleoprotein polypeptide A
Transporter activity	AF176008	−2.30	−2.12	−2.12	Mitochondrial carrier homolog 2
Transporter activity	BE275227	−1.98	−2.40	−1.88	Thioredoxin-like 4
Ubiquitin cycle	AL136812	−1.95	−2.21	−2.10	Makorin 1
Unclassified	AF017445	−2.22	−2.29	−2.72	Fucose-1-phosphate guanylyltransferase
Immune response (8)
Autoantigen	NM_006029	−2.19	−3.00	−2.22	Paraneoplastic Ag MA1
Cell adhesion	BG770327	−2.00	−2.26	−1.98	Galectin 3
Complement component	BF338113	−2.71	−2.14	−2.49	Complement component 4B
Kinase activity	AF153419	−4.36	−4.62	−5.15	Iκ B kinase complex-associated protein (IKBKAP)
MHC related	AK027789	−2.00	−2.38	−2.14	SIMP
MHC related	AL050135	−1.83	−1.83	−1.86	Regulatory factor X, 5
MHC related	BC008783	−2.67	−2.27	−2.26	HLA-B associated transcript 4
Transcriptional regulation	T27711	−1.84	−2.28	−2.32	BCL6A
Cellular/Intracellular signaling (9)
Cell adhesion	J03202	−1.92	−2.46	−2.26	Laminin B2 chain
Cytoskeleton	BC006141	−1.87	−2.18	−2.16	Erythrocyte protein band 4.1-like 3
Cytoskeleton	M69225	−2.14	−2.10	−2.11	Dystonin
GTPase activity	AK027730	−2.14	−2.28	−2.29	RAB2B, member RAS oncogene family
Kinase activity	BC001662	−2.07	−1.91	−2.02	MAPK-activated protein kinase 3
Kinase activity	BG391140	−1.82	−2.13	−2.03	c-src tyrosine kinase
Phosphatase	BC001095	−1.95	−1.92	−2.17	Protein phosphatase 2, regulatory subunit B, δ isoform
Protein interactions	BC009241	−2.36	−2.30	−1.88	TRK-fused gene
Receptor activity	AW020536	−2.17	−2.09	−1.96	Thyroid hormone receptor coactivating protein
Transcription (5)
Transcription factor activity	AB007885	−2.10	−2.08	−1.85	Zinc finger protein 262
Transcription factor activity	AB011102	−1.88	−2.30	−2.39	Zinc finger protein 292
Transcription factor activity	AF230388	−2.39	−2.43	−1.94	Tripartite motif-containing 29
Transcriptional regulation	BC004227	−2.17	−2.27	−1.80	Metastasis-associated family, member 3
Transcriptional regulation	BE254018	−2.12	−2.51	−2.16	SWI/SNF-related protein, subfamily d, member 2
Divers (4)
Unknown	AAH04632	−1.89	−2.19	−2.58	Ubxd4-related protein
Unknown	AF281064	−2.29	−1.80	−1.84	CHMP1.5 protein
Unknown	AK026058	−2.15	−2.35	−2.26	Clone HRC08294
Unknown	X75191	−1.92	−2.09	−1.84	Genomic YAC-end left arm of chromosome 15

^aThe 42 up-regulated and 39 down-regulated genes in MH, ML, and SN patients were manually classified. For each gene, we give the fold change for the different MG subgroup compared to non-MG adults.