Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation

Lee, Jamie A; Sinkovits, Robert S; Mock, Dennis; Rab, Eva L; Cai, Jennifer; Yang, Peng; Saunders, Brian; Hsueh, Robert C; Choi, Sangdun; Subramaniam, Shankar; Scheuermann, Richard H

doi:10.1186/1471-2105-7-237

Table 4 Manual curation of Gene Cluster #18 genes

From: Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation

	Protein description	Gene Sym Symbol	LocusLink ID	Function	Reference
A	CD72	Cd72	12517	BCR coreceptor	32–34 35
	dual specificity phosphatase 14	Dusp14	56405	lymphocyte signaling	36
	mitogen activated protein kinase kinase kinase kinase 1	Map4k1	26411	lymphocyte signaling	37–39
	mitogen activated protein kinase kinase 3	Map2k3	26397	lymphocyte signaling	40, 41
	serine/threonine kinase receptor associated protein	Strap	20901	TGFbeta signaling	42
	dishevelled associated activator of morphogenesis 1	Daam1	208846	Wnt signaling	43
	FK506 binding protein 1a	Fkbp1a	14225	BCR signaling/apoptosis	44–46
	nuclear factor of activated T-cells, cytoplasmic 2 interacting protein	Nfatc2ip	18020	BCR signaling/apoptosis	44–46
	sorting nexin 5	Snx5	69178	endocytosis	47, 48
	IQ motif containing GTPase activating protein 1	Iqgap1	29875	vesicle formation	49, 50
	amyotrophic lateral sclerosis 2 (juvenile) homolog (human)	Als2	74018	endosome fusion/Rab GEF	51, 52
	RAB18, RAS family	Rab18	19330	endocytosis/vesicle recycling	53–56 56
	RAB22, RAS family	Rab22a	19334	early endosome trafficking	56, 57
	Proton pump, subunit V0B (21 kDa)	Atp6v0b	114143	vesicle acidification	58–60
	Proton pump, subunit V1G1 (13 kDa)	Atp6v1g1	66290	vesicle acidification	58–60
	Proton pump, subunit V1C1 (42 kDa)	Atp6v1c1	66335	vesicle acidification	58–60
	similar to Proton pump, subunit V1F		76610	vesicle acidification	58–60
	Proton pump accessory protein 2	Atp6ap2	70495	vesicle acidification	61, 62
	Chloride channel 7	Clcn7	26373	vesicle pH regulation	63, 64
	dystrobrevin binding protein 1 (dysbindin)	Dtnbp1	94245	lysosome formation	65
	cystatin B	Cstb	13014	cathepsin protease inhibitor	66–68
	hexosaminidase A	Hexa	15211	hydrolase	69–71
	ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)	Cln3	12752	lysosome function	72
	HSP70 binding protein	Hspbp1	66245	Ag processing/loading	73
	similar to HSPC135		66067	chaperone (?), GTPase (?)
	HSPC245 homolog			chaperone (?)
	N-ethylmaleimide sensitive fusion protein attachment protein alpha	Napa	108124	vesicle fusion	74, 75
	RAB9, RAS family	Rab9	56382	vesicle tethering	76, 77
	activating transcription factor 1	Atf1	11908	MHC expression	78
	Sec61 alpha	Sec61a1	53421	ER translocation	79
	signal sequence receptor, alpha	Ssr1	107513	MHCII chaperone	80
	calmegin	Clgn	12745	MHC chaperone	81, 82
	similar to signal peptidase SPC22/23		76687	secretory protein processing	83
	vacuolar protein sorting 29	Vps29	56433	retrograde vesicle transport	84, 85
	reticulon 3	Rtn3	20168	exocytosis	86, 87
	tubulin, alpha 6	Tuba6	22146	cytoskeletal trafficking	88, 89
	CD63	Cd63	12512	MHCII coreceptor	90–92
	source of immunodominant MHC-associated peptides	Simp	68292	MHC peptide	93
B	24-dehydrocholesterol reductase	Dhcr24	74754	Cholesterol biosynthesis	94
	fatty acid binding protein 5, epidermal	Fabp5	16592	Fatty acid intracellular transport	95
	phosphatidylethanolamine binding protein	Pbp	23980	Membrane lipid transport	96
	prostaglandin D2 synthase 2, hematopoietic	Ptgds2	54486
	peroxisome biogenesis factor 1	Pex1	71382	Peroxisomal protein tranport	97
C	beclin 1 (coiled-coil, myosin-like BCL2-interacting protein)	Becn1	56208	Tumor suppression	98, 99
	caspase 4, apoptosis-related cysteine protease	Casp4	12363	Apoptosis	100–102
	Cd27 binding protein (Hindu God of destruction)	Siva	30954	Apoptosis	103, 104
D	polymyositis/scleroderma autoantigen 2	Pmscl2	50912	RNA processing autoantigen	105
	Sjogren's syndrome/scleroderma autoantigen 1 homolog (human)	Sssca1	56390	centromeric autoantigen	106
	amyotrophic lateral sclerosis 2 (juvenile) homolog (human)	Als2	74018	endosome fusion/Rab GEF	51, 52

Genes found in Gene Cluster #18 with functions related to (A) intracellular trafficking, BCR signaling, vesicle processing and function, and antigen processing and presentation, (C) apoptosis, and (D) B cell-related autoimmune disease. (B) Genes annotated with "transporter" activity whose roles are not yet known to be associated with intracellular trafficking.

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ISSN: 1471-2105

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