SZGR2

Summary ?

GeneID	928
Symbol	CD9
Synonyms	BTCC-1\|DRAP-27\|MIC3\|MRP-1\|TSPAN-29\|TSPAN29
Description	CD9 molecule
Reference	MIM:143030\|HGNC:HGNC:1709\|Ensembl:ENSG00000010278\|HPRD:00880\|Vega:OTTHUMG00000044400
Gene type	protein-coding
Map location	12p13.3
Pascal p-value	0.469
Sherlock p-value	0.381
Fetal beta	-2.102
DMG	1 (# studies)

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
DMG:Wockner_2014	Genome-wide DNA methylation analysis	This dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24).	2
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 2

Section I. Genetics and epigenetics annotation

DNM table

Gene	Chromosome	Position	Ref	Alt	Transcript	AA change	Mutation type	Sift	CG46	Trait	Study
CD9	chr12	6334597	C	T	NM_001769	.	silent			Schizophrenia	DNM:Fromer_2014

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg19615684	12	6310744	CD9	2.057E-4	-0.504	0.035	DMG:Wockner_2014
cg02586910	12	6314603	CD9	5.207E-4	-0.712	0.048	DMG:Wockner_2014

Section II. Transcriptome annotation

General gene expression (GTEx)

Gene expression during devlopment (BrainCloud)

Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.

Gene expression of temporal and spatial changes (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
TMEM63A	0.92	0.92
PCTK3	0.90	0.94
AC087645.1	0.90	0.95
ATPGD1	0.90	0.93
PLXNB3	0.90	0.91
CERCAM	0.89	0.55
SEMA3B	0.88	0.86
ERBB3	0.88	0.90
P2RX7	0.88	0.84
LDB3	0.88	0.91

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
MED19	-0.50	-0.75
STMN1	-0.49	-0.76
RPL12	-0.49	-0.78
POLB	-0.49	-0.77
NKIRAS2	-0.49	-0.71
ALKBH2	-0.49	-0.79
IFT52	-0.48	-0.77
NR2C2AP	-0.48	-0.78
HN1	-0.48	-0.76
RARS2	-0.48	-0.75

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005515	protein binding	IEA		-
GO:0005515	protein binding	IPI		11278880 \|11504738
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0030913	paranodal junction assembly	IEA	axon, Glial (GO term level: 15)	-
GO:0030913	paranodal junction assembly	ISS	axon, Glial (GO term level: 15)	-
GO:0007155	cell adhesion	IDA		7511626
GO:0008285	negative regulation of cell proliferation	IEA		-
GO:0030168	platelet activation	NAS		2037603
GO:0006928	cell motion	IDA		8478605
GO:0007342	fusion of sperm to egg plasma membrane	IDA		14575715
GO:0007342	fusion of sperm to egg plasma membrane	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0016020	membrane	IEA		-
GO:0016021	integral to membrane	IEA		-
GO:0005886	plasma membrane	EXP		10515286
GO:0005886	plasma membrane	NAS		6198179
GO:0005887	integral to plasma membrane	NAS		2037603
GO:0031092	platelet alpha granule membrane	EXP		10515286

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
ADAM2	CRYN1 \| CRYN2 \| FTNB \| PH-30b \| PH30	ADAM metallopeptidase domain 2	-	HPRD	10518536
CD19	B4 \| MGC12802	CD19 molecule	-	HPRD,BioGRID	9804823
CD36	CHDS7 \| FAT \| GP3B \| GP4 \| GPIV \| PASIV \| SCARB3	CD36 molecule (thrombospondin receptor)	-	HPRD,BioGRID	11238109
CD46	MCP \| MGC26544 \| MIC10 \| TLX \| TRA2.10	CD46 molecule, complement regulatory protein	Affinity Capture-Western	BioGRID	10741407
CD53	MOX44 \| TSPAN25	CD53 molecule	-	HPRD,BioGRID	11959120
CD59	16.3A5 \| 1F5 \| EJ16 \| EJ30 \| EL32 \| FLJ38134 \| FLJ92039 \| G344 \| HRF-20 \| HRF20 \| MAC-IP \| MACIF \| MEM43 \| MGC2354 \| MIC11 \| MIN1 \| MIN2 \| MIN3 \| MIRL \| MSK21 \| p18-20	CD59 molecule, complement regulatory protein	-	HPRD	1377690
CD63	LAMP-3 \| ME491 \| MLA1 \| OMA81H \| TSPAN30	CD63 molecule	-	HPRD,BioGRID	8630057 \|11204565 \|12175627
CD81	S5.7 \| TAPA1 \| TSPAN28	CD81 molecule	-	HPRD	12036870
CD81	S5.7 \| TAPA1 \| TSPAN28	CD81 molecule	Affinity Capture-Western Co-fractionation	BioGRID	8630057 \|9804823
CD82	4F9 \| C33 \| GR15 \| IA4 \| KAI1 \| R2 \| SAR2 \| ST6 \| TSPAN27	CD82 molecule	Affinity Capture-Western	BioGRID	15492270
IGSF8	CD316 \| CD81P3 \| EWI2 \| PGRL	immunoglobulin superfamily, member 8	-	HPRD,BioGRID	11504738
ITGA3	CD49C \| FLJ34631 \| FLJ34704 \| GAP-B3 \| GAPB3 \| MSK18 \| VCA-2 \| VL3A \| VLA3a	integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)	-	HPRD,BioGRID	10065872 \|10694273
ITGA5	CD49e \| FNRA \| VLA5A	integrin, alpha 5 (fibronectin receptor, alpha polypeptide)	-	HPRD,BioGRID	10065872
ITGB1	CD29 \| FNRB \| GPIIA \| MDF2 \| MSK12 \| VLA-BETA \| VLAB	integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)	Affinity Capture-Western	BioGRID	8630057 \|12175627
KIT	C-Kit \| CD117 \| PBT \| SCFR	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	-	HPRD,BioGRID	12036870
PRKCA	AAG6 \| MGC129900 \| MGC129901 \| PKC-alpha \| PKCA \| PRKACA	protein kinase C, alpha	-	HPRD,BioGRID	11325968
PTGFRN	CD315 \| CD9P-1 \| EWI-F \| FLJ11001 \| FPRP \| KIAA1436 \| SMAP-6	prostaglandin F2 receptor negative regulator	-	HPRD,BioGRID	11087758 \|11278880
SERPINH1	AsTP3 \| CBP1 \| CBP2 \| HSP47 \| PIG14 \| PPROM \| RA-A47 \| SERPINH2 \| gp46	serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	-	HPRD,BioGRID	10227388
TSPAN4	NAG-2 \| NAG2 \| TETRASPAN \| TM4SF7 \| TSPAN-4	tetraspanin 4	-	HPRD,BioGRID	9360996

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG HEMATOPOIETIC CELL LINEAGE	88	60	All SZGR 2.0 genes in this pathway
PID A6B1 A6B4 INTEGRIN PATHWAY	46	35	All SZGR 2.0 genes in this pathway
REACTOME RESPONSE TO ELEVATED PLATELET CYTOSOLIC CA2	89	56	All SZGR 2.0 genes in this pathway
REACTOME HEMOSTASIS	466	331	All SZGR 2.0 genes in this pathway
REACTOME PLATELET ACTIVATION SIGNALING AND AGGREGATION	208	138	All SZGR 2.0 genes in this pathway
KORKOLA EMBRYONAL CARCINOMA UP	41	27	All SZGR 2.0 genes in this pathway
KORKOLA CHORIOCARCINOMA UP	6	5	All SZGR 2.0 genes in this pathway
KORKOLA SEMINOMA UP	44	27	All SZGR 2.0 genes in this pathway
HOLLMANN APOPTOSIS VIA CD40 DN	267	178	All SZGR 2.0 genes in this pathway
DAVICIONI PAX FOXO1 SIGNATURE IN ARMS UP	59	38	All SZGR 2.0 genes in this pathway
WATANABE COLON CANCER MSI VS MSS DN	81	42	All SZGR 2.0 genes in this pathway
ZHONG RESPONSE TO AZACITIDINE AND TSA UP	183	119	All SZGR 2.0 genes in this pathway
DAVICIONI TARGETS OF PAX FOXO1 FUSIONS UP	255	177	All SZGR 2.0 genes in this pathway
DAVICIONI RHABDOMYOSARCOMA PAX FOXO1 FUSION UP	64	37	All SZGR 2.0 genes in this pathway
HUTTMANN B CLL POOR SURVIVAL UP	276	187	All SZGR 2.0 genes in this pathway
VECCHI GASTRIC CANCER EARLY UP	430	232	All SZGR 2.0 genes in this pathway
SMIRNOV CIRCULATING ENDOTHELIOCYTES IN CANCER UP	158	103	All SZGR 2.0 genes in this pathway
OSWALD HEMATOPOIETIC STEM CELL IN COLLAGEN GEL DN	275	168	All SZGR 2.0 genes in this pathway
TAKEDA TARGETS OF NUP98 HOXA9 FUSION 8D DN	205	127	All SZGR 2.0 genes in this pathway
TAKEDA TARGETS OF NUP98 HOXA9 FUSION 10D DN	142	90	All SZGR 2.0 genes in this pathway
RHEIN ALL GLUCOCORTICOID THERAPY DN	362	238	All SZGR 2.0 genes in this pathway
LEE NEURAL CREST STEM CELL DN	118	79	All SZGR 2.0 genes in this pathway
CHIARADONNA NEOPLASTIC TRANSFORMATION KRAS CDC25 UP	58	39	All SZGR 2.0 genes in this pathway
CHIARADONNA NEOPLASTIC TRANSFORMATION KRAS DN	142	95	All SZGR 2.0 genes in this pathway
CHIARADONNA NEOPLASTIC TRANSFORMATION CDC25 DN	153	100	All SZGR 2.0 genes in this pathway
LANDIS ERBB2 BREAST TUMORS 65 UP	22	13	All SZGR 2.0 genes in this pathway
OUELLET OVARIAN CANCER INVASIVE VS LMP UP	117	85	All SZGR 2.0 genes in this pathway
LANDIS ERBB2 BREAST TUMORS 324 UP	150	93	All SZGR 2.0 genes in this pathway
MISSIAGLIA REGULATED BY METHYLATION UP	126	78	All SZGR 2.0 genes in this pathway
JOHANSSON GLIOMAGENESIS BY PDGFB UP	58	44	All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL BREAST 4 5WK UP	271	175	All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL TGFB1 TARGETS DN	62	44	All SZGR 2.0 genes in this pathway
OLSSON E2F3 TARGETS DN	49	33	All SZGR 2.0 genes in this pathway
SCHLOSSER SERUM RESPONSE DN	712	443	All SZGR 2.0 genes in this pathway
GRUETZMANN PANCREATIC CANCER UP	358	245	All SZGR 2.0 genes in this pathway
SHETH LIVER CANCER VS TXNIP LOSS PAM1	229	137	All SZGR 2.0 genes in this pathway
ONDER CDH1 TARGETS 2 DN	464	276	All SZGR 2.0 genes in this pathway
LE EGR2 TARGETS DN	108	84	All SZGR 2.0 genes in this pathway
STANELLE E2F1 TARGETS	29	20	All SZGR 2.0 genes in this pathway
TARTE PLASMA CELL VS PLASMABLAST UP	398	262	All SZGR 2.0 genes in this pathway
UEDA PERIFERAL CLOCK	169	111	All SZGR 2.0 genes in this pathway
TENEDINI MEGAKARYOCYTE MARKERS	66	48	All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT REJECTED VS OK DN	546	351	All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT OK VS DONOR UP	555	346	All SZGR 2.0 genes in this pathway
HADDAD B LYMPHOCYTE PROGENITOR	293	193	All SZGR 2.0 genes in this pathway
IGLESIAS E2F TARGETS UP	151	103	All SZGR 2.0 genes in this pathway
BRUNO HEMATOPOIESIS	66	48	All SZGR 2.0 genes in this pathway
KUMAR TARGETS OF MLL AF9 FUSION	405	264	All SZGR 2.0 genes in this pathway
SESTO RESPONSE TO UV C4	20	14	All SZGR 2.0 genes in this pathway
WANG SMARCE1 TARGETS DN	371	218	All SZGR 2.0 genes in this pathway
CHIBA RESPONSE TO TSA UP	52	33	All SZGR 2.0 genes in this pathway
MACLACHLAN BRCA1 TARGETS DN	16	12	All SZGR 2.0 genes in this pathway
LINDVALL IMMORTALIZED BY TERT UP	78	48	All SZGR 2.0 genes in this pathway
MURAKAMI UV RESPONSE 6HR UP	37	31	All SZGR 2.0 genes in this pathway
WESTON VEGFA TARGETS	108	71	All SZGR 2.0 genes in this pathway
GERHOLD ADIPOGENESIS DN	64	44	All SZGR 2.0 genes in this pathway
LEE AGING NEOCORTEX UP	89	59	All SZGR 2.0 genes in this pathway
WELCSH BRCA1 TARGETS UP	198	132	All SZGR 2.0 genes in this pathway
KEEN RESPONSE TO ROSIGLITAZONE DN	106	68	All SZGR 2.0 genes in this pathway
DEBIASI APOPTOSIS BY REOVIRUS INFECTION DN	287	208	All SZGR 2.0 genes in this pathway
JIANG HYPOXIA NORMAL	311	205	All SZGR 2.0 genes in this pathway
WANG CISPLATIN RESPONSE AND XPC UP	202	115	All SZGR 2.0 genes in this pathway
HAN JNK SINGALING DN	39	27	All SZGR 2.0 genes in this pathway
WESTON VEGFA TARGETS 3HR	74	47	All SZGR 2.0 genes in this pathway
ZHONG SECRETOME OF LUNG CANCER AND FIBROBLAST	132	93	All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS UP	317	208	All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS SILENCED BY METHYLATION UP	461	298	All SZGR 2.0 genes in this pathway
SARRIO EPITHELIAL MESENCHYMAL TRANSITION DN	154	101	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER UP	973	570	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE UP	863	514	All SZGR 2.0 genes in this pathway
MITSIADES RESPONSE TO APLIDIN DN	249	165	All SZGR 2.0 genes in this pathway
BOCHKIS FOXA2 TARGETS	425	261	All SZGR 2.0 genes in this pathway
MATZUK FERTILIZATION	8	5	All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL CULTURED VS FRESH UP	425	298	All SZGR 2.0 genes in this pathway
CONRAD STEM CELL	39	27	All SZGR 2.0 genes in this pathway
WANG TUMOR INVASIVENESS DN	210	128	All SZGR 2.0 genes in this pathway
BOYLAN MULTIPLE MYELOMA C D DN	252	155	All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO CSF2RB AND IL4 UP	338	225	All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO HGF UP	418	282	All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO HGF VS CSF2RB AND IL4 UP	408	276	All SZGR 2.0 genes in this pathway
VANASSE BCL2 TARGETS DN	74	50	All SZGR 2.0 genes in this pathway
SWEET LUNG CANCER KRAS UP	491	316	All SZGR 2.0 genes in this pathway
HINATA NFKB TARGETS KERATINOCYTE UP	91	63	All SZGR 2.0 genes in this pathway
HINATA NFKB TARGETS FIBROBLAST UP	84	60	All SZGR 2.0 genes in this pathway
HOFFMANN PRE BI TO LARGE PRE BII LYMPHOCYTE DN	75	61	All SZGR 2.0 genes in this pathway
HOFMANN MYELODYSPLASTIC SYNDROM RISK UP	24	14	All SZGR 2.0 genes in this pathway
CHEN METABOLIC SYNDROM NETWORK	1210	725	All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K4ME3 AND H3K27ME3	1069	729	All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA CHEMOTAXIS DN	457	302	All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA HAPTOTAXIS DN	668	419	All SZGR 2.0 genes in this pathway
JISON SICKLE CELL DISEASE UP	181	106	All SZGR 2.0 genes in this pathway
YAGI AML WITH INV 16 TRANSLOCATION	422	277	All SZGR 2.0 genes in this pathway
BOYLAN MULTIPLE MYELOMA PCA1 UP	101	66	All SZGR 2.0 genes in this pathway
MURAKAMI UV RESPONSE 1HR UP	17	10	All SZGR 2.0 genes in this pathway
LI INDUCED T TO NATURAL KILLER UP	307	182	All SZGR 2.0 genes in this pathway
STAMBOLSKY TARGETS OF MUTATED TP53 DN	50	24	All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS OLIGODENDROCYTE NUMBER CORR UP	756	494	All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS CONFLUENT	567	365	All SZGR 2.0 genes in this pathway
FIGUEROA AML METHYLATION CLUSTER 1 UP	125	61	All SZGR 2.0 genes in this pathway
WIERENGA STAT5A TARGETS DN	213	127	All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 3 UP	430	288	All SZGR 2.0 genes in this pathway
ISSAEVA MLL2 TARGETS	62	35	All SZGR 2.0 genes in this pathway
DELPUECH FOXO3 TARGETS UP	68	49	All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION DN	1080	713	All SZGR 2.0 genes in this pathway
FORTSCHEGGER PHF8 TARGETS DN	784	464	All SZGR 2.0 genes in this pathway
RATTENBACHER BOUND BY CELF1	467	251	All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA family	Target position			miRNA ID	miRNA seq
miRNA family	UTR start	UTR end	Match method	miRNA ID	miRNA seq
miR-370	19	25	1A	hsa-miR-370^brain	GCCUGCUGGGGUGGAACCUGG

SZ: miRNAs which differentially expressed in brain cortex of schizophrenia patients comparing with control samples using microarray. Click here to see the list of SZ related miRNAs.
Brain: miRNAs which are expressed in brain based on miRNA microarray expression studies. Click here to see the list of brain related miRNAs.

Gene Page: CD9