SZGR2

Summary ?

GeneID	920
Symbol	CD4
Synonyms	CD4mut
Description	CD4 molecule
Reference	MIM:186940\|HGNC:HGNC:1678\|Ensembl:ENSG00000010610\|HPRD:01740\|Vega:OTTHUMG00000168514
Gene type	protein-coding
Map location	12p13.31
Pascal p-value	0.02
Sherlock p-value	0.001
Fetal beta	-0.418

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
PMID:cooccur	High-throughput literature-search	Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
Association	A combined odds ratio method (Sun et al. 2008), association studies	1	Link to SZGene
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophrenics,schizophrenias	Click to show details
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 1

Section I. Genetics and epigenetics annotation

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
RNF44	0.68	0.71
SCMH1	0.67	0.70
STK11IP	0.66	0.68
NPHP4	0.65	0.67
MPPE1	0.65	0.69
TAOK2	0.65	0.66
ULK1	0.65	0.68
CCRK	0.65	0.67
ZMIZ2	0.65	0.70
TAF6	0.64	0.68

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AF347015.31	-0.53	-0.55
AF347015.21	-0.52	-0.56
MT-CO2	-0.51	-0.53
AL139819.3	-0.50	-0.55
AF347015.2	-0.49	-0.50
MT-CYB	-0.48	-0.51
AF347015.8	-0.48	-0.51
GNG11	-0.47	-0.55
HIGD1B	-0.47	-0.51
AF347015.26	-0.46	-0.47

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0004888	transmembrane receptor activity	TAS		10358157
GO:0001948	glycoprotein binding	IPI		10922058
GO:0005201	extracellular matrix structural constituent	NAS		12444132
GO:0008270	zinc ion binding	IDA		9668045
GO:0042289	MHC class II protein binding	NAS		8512039
GO:0015026	coreceptor activity	NAS		8512039
GO:0042803	protein homodimerization activity	IDA		12444132
GO:0019901	protein kinase binding	IPI		7486703
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0000747	conjugation with cellular fusion	IDA		9166430
GO:0001816	cytokine production	IEA		-
GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	NAS		8512039
GO:0007155	cell adhesion	IEA		-
GO:0006955	immune response	NAS		8512039
GO:0019059	initiation of viral infection	EXP		12091904
GO:0050870	positive regulation of T cell activation	IEA		-
GO:0045860	positive regulation of protein kinase activity	IDA		2118992
GO:0050731	positive regulation of peptidyl-tyrosine phosphorylation	IEA		-
GO:0050850	positive regulation of calcium-mediated signaling	IEA		-
GO:0045086	positive regulation of interleukin-2 biosynthetic process	NAS		1901411
GO:0045058	T cell selection	IDA		9551897
GO:0044419	interspecies interaction between organisms	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0042101	T cell receptor complex	NAS	Synap (GO term level: 8)	8512039
GO:0005789	endoplasmic reticulum membrane	EXP		9660940
GO:0005769	early endosome	EXP		2014052 \|15202998
GO:0016021	integral to membrane	IEA		-
GO:0009897	external side of plasma membrane	IEA		-
GO:0005886	plasma membrane	EXP		2014052 \|11048639 \|11827988 \|15202998 \|15489916 \|17652306
GO:0005886	plasma membrane	IDA		8124721

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
BTRC	BETA-TRCP \| FBW1A \| FBXW1 \| FBXW1A \| FWD1 \| MGC4643 \| bTrCP \| bTrCP1 \| betaTrCP	beta-transducin repeat containing	-	HPRD,BioGRID	9660940
CCR5	CC-CKR-5 \| CCCKR5 \| CD195 \| CKR-5 \| CKR5 \| CMKBR5	chemokine (C-C motif) receptor 5	-	HPRD,BioGRID	10816381
CD2	SRBC \| T11	CD2 molecule	-	HPRD	7539755
CD28	MGC138290 \| Tp44	CD28 molecule	-	HPRD	7539755
CD38	T10	CD38 molecule	-	HPRD	7539755
CD4	CD4mut	CD4 molecule	CD4 forms homodimers.	BIND	12444132
CD44	CDW44 \| CSPG8 \| ECMR-III \| HCELL \| IN \| LHR \| MC56 \| MDU2 \| MDU3 \| MGC10468 \| MIC4 \| MUTCH-I \| Pgp1	CD44 molecule (Indian blood group)	-	HPRD	7539755
CD5	LEU1 \| T1	CD5 molecule	-	HPRD	7539755
CD53	MOX44 \| TSPAN25	CD53 molecule	-	HPRD	7539755
CD81	S5.7 \| TAPA1 \| TSPAN28	CD81 molecule	Affinity Capture-Western	BioGRID	7636191
CD82	4F9 \| C33 \| GR15 \| IA4 \| KAI1 \| R2 \| SAR2 \| ST6 \| TSPAN27	CD82 molecule	-	HPRD,BioGRID	7636191
CTSD	CLN10 \| CPSD \| MGC2311	cathepsin D	-	HPRD	11581410
CXCL12	PBSF \| SCYB12 \| SDF-1a \| SDF-1b \| SDF1 \| SDF1A \| SDF1B \| TLSF-a \| TLSF-b \| TPAR1	chemokine (C-X-C motif) ligand 12 (stromal cell-derived factor 1)	-	HPRD	10600606
CXCR4	CD184 \| D2S201E \| FB22 \| HM89 \| HSY3RR \| LAP3 \| LCR1 \| LESTR \| NPY3R \| NPYR \| NPYRL \| NPYY3R \| WHIM	chemokine (C-X-C motif) receptor 4	Affinity Capture-Western	BioGRID	10816381
FCGR3A	CD16 \| CD16A \| FCG3 \| FCGR3 \| FCGRIII \| FCR-10 \| FCRIII \| FCRIIIA \| IGFR3	Fc fragment of IgG, low affinity IIIa, receptor (CD16a)	-	HPRD	11756173
HLA-DPA1	HLA-DP1A \| HLADP \| HLASB	major histocompatibility complex, class II, DP alpha 1	-	HPRD	12899833
HLA-DQA2	HLA-DXA	major histocompatibility complex, class II, DQ alpha 2	-	HPRD	11535811
IL16	FLJ16806 \| FLJ42735 \| FLJ44234 \| HsT19289 \| IL-16 \| LCF \| prIL-16	interleukin 16 (lymphocyte chemoattractant factor)	-	HPRD,BioGRID	1851800\|7910967
IL2RA	CD25 \| IDDM10 \| IL2R \| TCGFR	interleukin 2 receptor, alpha	-	HPRD	7539755
KCNAB2	AKR6A5 \| HKvbeta2 \| HKvbeta2.1 \| HKvbeta2.2 \| KCNA2B \| KV-BETA-2 \| MGC117289	potassium voltage-gated channel, shaker-related subfamily, beta member 2	Affinity Capture-Western	BioGRID	12893943
LAT	LAT1 \| pp36	linker for activation of T cells	-	HPRD	10562325
LCK	YT16 \| p56lck \| pp58lck	lymphocyte-specific protein tyrosine kinase	-	HPRD,BioGRID	11854499
LGALS1	DKFZp686E23103 \| GAL1 \| GBP	lectin, galactoside-binding, soluble, 1	in vitro	BioGRID	10490978
MARCH4	MARCH-IV \| MGC104908 \| RNF174	membrane-associated ring finger (C3HC4) 4	-	HPRD	14722266
PI4KA	FLJ16556 \| PI4K-ALPHA \| PIK4CA \| pi4K230	phosphatidylinositol 4-kinase, catalytic, alpha	-	HPRD	8246987
PIK3R1	GRB1 \| p85 \| p85-ALPHA	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	-	HPRD	8246987
PIP	GCDFP-15 \| GCDFP15 \| GPIP4	prolactin-induced protein	-	HPRD,BioGRID	10820003
PTK2	FADK \| FAK \| FAK1 \| pp125FAK	PTK2 protein tyrosine kinase 2	-	HPRD	10384144
PTPRC	B220 \| CD45 \| CD45R \| GP180 \| LCA \| LY5 \| T200	protein tyrosine phosphatase, receptor type, C	-	HPRD,BioGRID	1834739
SELL	CD62L \| LAM-1 \| LAM1 \| LECAM1 \| LNHR \| LSEL \| LYAM1 \| Leu-8 \| Lyam-1 \| PLNHR \| TQ1 \| hLHRc	selectin L	-	HPRD	7539755
SPG21	ACP33 \| BM-019 \| GL010 \| MASPARDIN \| MAST	spastic paraplegia 21 (autosomal recessive, Mast syndrome)	-	HPRD,BioGRID	11113139
TNFRSF10A	APO2 \| CD261 \| DR4 \| MGC9365 \| TRAILR-1 \| TRAILR1	tumor necrosis factor receptor superfamily, member 10a	-	HPRD	7650480
UNC119	HRG4	unc-119 homolog (C. elegans)	-	HPRD,BioGRID	14757743

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG CELL ADHESION MOLECULES CAMS	134	93	All SZGR 2.0 genes in this pathway
KEGG ANTIGEN PROCESSING AND PRESENTATION	89	65	All SZGR 2.0 genes in this pathway
KEGG HEMATOPOIETIC CELL LINEAGE	88	60	All SZGR 2.0 genes in this pathway
KEGG T CELL RECEPTOR SIGNALING PATHWAY	108	89	All SZGR 2.0 genes in this pathway
KEGG PRIMARY IMMUNODEFICIENCY	35	28	All SZGR 2.0 genes in this pathway
BIOCARTA CSK PATHWAY	24	20	All SZGR 2.0 genes in this pathway
BIOCARTA ASBCELL PATHWAY	12	11	All SZGR 2.0 genes in this pathway
BIOCARTA INFLAM PATHWAY	29	24	All SZGR 2.0 genes in this pathway
BIOCARTA TCAPOPTOSIS PATHWAY	11	8	All SZGR 2.0 genes in this pathway
BIOCARTA IL17 PATHWAY	17	12	All SZGR 2.0 genes in this pathway
BIOCARTA IL5 PATHWAY	10	9	All SZGR 2.0 genes in this pathway
BIOCARTA TCRA PATHWAY	13	10	All SZGR 2.0 genes in this pathway
BIOCARTA NO2IL12 PATHWAY	17	14	All SZGR 2.0 genes in this pathway
BIOCARTA STEM PATHWAY	15	13	All SZGR 2.0 genes in this pathway
BIOCARTA NKT PATHWAY	29	21	All SZGR 2.0 genes in this pathway
BIOCARTA THELPER PATHWAY	14	11	All SZGR 2.0 genes in this pathway
PID TCR PATHWAY	66	51	All SZGR 2.0 genes in this pathway
PID IL12 2PATHWAY	63	54	All SZGR 2.0 genes in this pathway
PID CXCR4 PATHWAY	102	78	All SZGR 2.0 genes in this pathway
PID CMYB PATHWAY	84	61	All SZGR 2.0 genes in this pathway
PID IL23 PATHWAY	37	30	All SZGR 2.0 genes in this pathway
PID ARF 3PATHWAY	19	13	All SZGR 2.0 genes in this pathway
PID HES HEY PATHWAY	48	39	All SZGR 2.0 genes in this pathway
PID IL12 STAT4 PATHWAY	33	29	All SZGR 2.0 genes in this pathway
REACTOME NEF MEDIATES DOWN MODULATION OF CELL SURFACE RECEPTORS BY RECRUITING THEM TO CLATHRIN ADAPTERS	21	12	All SZGR 2.0 genes in this pathway
REACTOME DEFENSINS	51	12	All SZGR 2.0 genes in this pathway
REACTOME TCR SIGNALING	54	46	All SZGR 2.0 genes in this pathway
REACTOME DOWNSTREAM TCR SIGNALING	37	32	All SZGR 2.0 genes in this pathway
REACTOME PHOSPHORYLATION OF CD3 AND TCR ZETA CHAINS	16	15	All SZGR 2.0 genes in this pathway
REACTOME TRANSLOCATION OF ZAP 70 TO IMMUNOLOGICAL SYNAPSE	14	14	All SZGR 2.0 genes in this pathway
REACTOME GENERATION OF SECOND MESSENGER MOLECULES	27	25	All SZGR 2.0 genes in this pathway
REACTOME PD1 SIGNALING	18	14	All SZGR 2.0 genes in this pathway
REACTOME COSTIMULATION BY THE CD28 FAMILY	63	48	All SZGR 2.0 genes in this pathway
REACTOME HIV INFECTION	207	122	All SZGR 2.0 genes in this pathway
REACTOME HIV LIFE CYCLE	125	69	All SZGR 2.0 genes in this pathway
REACTOME EARLY PHASE OF HIV LIFE CYCLE	21	8	All SZGR 2.0 genes in this pathway
REACTOME HOST INTERACTIONS OF HIV FACTORS	132	81	All SZGR 2.0 genes in this pathway
REACTOME INNATE IMMUNE SYSTEM	279	178	All SZGR 2.0 genes in this pathway
REACTOME THE ROLE OF NEF IN HIV1 REPLICATION AND DISEASE PATHOGENESIS	28	19	All SZGR 2.0 genes in this pathway
REACTOME IMMUNE SYSTEM	933	616	All SZGR 2.0 genes in this pathway
REACTOME ADAPTIVE IMMUNE SYSTEM	539	350	All SZGR 2.0 genes in this pathway
FULCHER INFLAMMATORY RESPONSE LECTIN VS LPS DN	463	290	All SZGR 2.0 genes in this pathway
ENK UV RESPONSE KERATINOCYTE UP	530	342	All SZGR 2.0 genes in this pathway
SHANK TAL1 TARGETS DN	10	6	All SZGR 2.0 genes in this pathway
LIU NASOPHARYNGEAL CARCINOMA	70	38	All SZGR 2.0 genes in this pathway
KENNY CTNNB1 TARGETS DN	52	34	All SZGR 2.0 genes in this pathway
NGUYEN NOTCH1 TARGETS UP	29	23	All SZGR 2.0 genes in this pathway
NIELSEN GIST AND SYNOVIAL SARCOMA DN	20	15	All SZGR 2.0 genes in this pathway
LEE AGING CEREBELLUM DN	86	66	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 48HR UP	180	125	All SZGR 2.0 genes in this pathway
MCLACHLAN DENTAL CARIES DN	245	144	All SZGR 2.0 genes in this pathway
MCLACHLAN DENTAL CARIES UP	253	147	All SZGR 2.0 genes in this pathway
LEE LIVER CANCER	49	29	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER NORMAL LIKE UP	476	285	All SZGR 2.0 genes in this pathway
WILENSKY RESPONSE TO DARAPLADIB	29	20	All SZGR 2.0 genes in this pathway
QI PLASMACYTOMA UP	259	185	All SZGR 2.0 genes in this pathway
FONTAINE THYROID TUMOR UNCERTAIN MALIGNANCY UP	36	23	All SZGR 2.0 genes in this pathway
FONTAINE PAPILLARY THYROID CARCINOMA UP	66	38	All SZGR 2.0 genes in this pathway
MOOTHA GLUCONEOGENESIS	32	23	All SZGR 2.0 genes in this pathway
MOOTHA GLYCOLYSIS	21	13	All SZGR 2.0 genes in this pathway
NIELSEN SYNOVIAL SARCOMA DN	20	13	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 1HR UP	61	44	All SZGR 2.0 genes in this pathway
VERHAAK GLIOBLASTOMA MESENCHYMAL	216	130	All SZGR 2.0 genes in this pathway
WANG RESPONSE TO GSK3 INHIBITOR SB216763 UP	397	206	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-181	74	81	1A,m8	hsa-miR-181a^brain	AACAUUCAACGCUGUCGGUGAGU
				hsa-miR-181b^SZ	AACAUUCAUUGCUGUCGGUGGG
				hsa-miR-181c^brain	AACAUUCAACCUGUCGGUGAGU
				hsa-miR-181d^brain	AACAUUCAUUGUUGUCGGUGGGUU
miR-221/222	77	84	1A,m8	hsa-miR-221^brain	AGCUACAUUGUCUGCUGGGUUUC
miR-221/222	77	84	1A,m8	hsa-miR-222^brain	AGCUACAUCUGGCUACUGGGUCUC

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: CD4