SZGR2

Summary ?

GeneID	6386
Symbol	SDCBP
Synonyms	MDA-9\|MDA9\|ST1\|SYCL\|TACIP18
Description	syndecan binding protein
Reference	MIM:602217\|HGNC:HGNC:10662\|Ensembl:ENSG00000137575\|HPRD:03741\|Vega:OTTHUMG00000164303
Gene type	protein-coding
Map location	8q12
Pascal p-value	0.561
Sherlock p-value	0.16
Fetal beta	1.285
DMG	1 (# studies)
eGene	Cerebellum Frontal Cortex BA9 Meta
Support	Potential synaptic genes

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
DMG:Nishioka_2013	Genome-wide DNA methylation analysis	The authors investigated the methylation profiles of DNA in peripheral blood cells from 18 patients with first-episode schizophrenia (FESZ) and from 15 normal controls.	1
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 1
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 1.0012

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg02103294	8	59465971	SDCBP		-0.026	0.25	DMG:Nishioka_2013

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
C6orf167	0.92	0.80
DTL	0.91	0.67
TIMELESS	0.90	0.80
MCM2	0.90	0.79
CDK2	0.89	0.52
MCM10	0.89	0.61
BRCA2	0.89	0.59
MCM5	0.89	0.76
RRM2	0.89	0.61
FAM83D	0.89	0.75

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
C5orf53	-0.41	-0.62
PTH1R	-0.40	-0.63
SLC9A3R2	-0.40	-0.35
SLC16A11	-0.39	-0.49
LGI4	-0.38	-0.36
AIFM3	-0.38	-0.56
HLA-F	-0.38	-0.54
TNFSF12	-0.38	-0.52
FXYD7	-0.38	-0.33
TMEM54	-0.38	-0.48

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005137	interleukin-5 receptor binding	ISS		11498591
GO:0005515	protein binding	IEA		-
GO:0008093	cytoskeletal adaptor activity	NAS		9391086
GO:0016491	oxidoreductase activity	IEA		-
GO:0045545	syndecan binding	NAS		9391086
GO:0047485	protein N-terminus binding	IPI		15371445
GO:0046982	protein heterodimerization activity	IPI		11152476
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007268	synaptic transmission	NAS	neuron, Synap, Neurotransmitter (GO term level: 6)	9883737
GO:0007265	Ras protein signal transduction	IEA		-
GO:0007242	intracellular signaling cascade	NAS		9391086
GO:0008152	metabolic process	IEA		-
GO:0006930	substrate-bound cell migration, cell extension	NAS		12037664
GO:0006612	protein targeting to membrane	NAS		10230395
GO:0030036	actin cytoskeleton organization	NAS		12037664
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005856	cytoskeleton	NAS		9391086
GO:0005789	endoplasmic reticulum membrane	IEA		-
GO:0005634	nucleus	NAS		11179419
GO:0005737	cytoplasm	IEA		-
GO:0005783	endoplasmic reticulum	IEA		-
GO:0005912	adherens junction	NAS		11179419
GO:0005895	interleukin-5 receptor complex	ISS		11498591
GO:0005886	plasma membrane	IEA		-
GO:0042470	melanosome	IEA		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
CADM1	BL2 \| DKFZp686F1789 \| IGSF4 \| IGSF4A \| MGC149785 \| MGC51880 \| NECL2 \| Necl-2 \| RA175 \| ST17 \| SYNCAM \| TSLC1 \| sTSLC-1 \| sgIGSF \| synCAM1	cell adhesion molecule 1	-	HPRD,BioGRID	12202822
EFNB1	CFND \| CFNS \| EFL3 \| EPLG2 \| Elk-L \| LERK2 \| MGC8782	ephrin-B1	-	HPRD,BioGRID	9920925
EFNB2	EPLG5 \| HTKL \| Htk-L \| LERK5 \| MGC126226 \| MGC126227 \| MGC126228	ephrin-B2	Ephrin-B2 interacts with ST-1. This interaction was modelled on a demonstrated interaction between human Ephrin-B2 and rat ST-1.	BIND	11152476
EFNB2	EPLG5 \| HTKL \| Htk-L \| LERK5 \| MGC126226 \| MGC126227 \| MGC126228	ephrin-B2	-	HPRD	10473577
EPHA7	EHK3 \| HEK11	EPH receptor A7	EphA7 interacts with ST-1. This interaction was modelled on a demonstrated interaction between human EphA7 and rat ST-1.	BIND	11152476
GRIA1	GLUH1 \| GLUR1 \| GLURA \| HBGR1 \| MGC133252	glutamate receptor, ionotropic, AMPA 1	-	HPRD,BioGRID	11891216
GRIA2	GLUR2 \| GLURB \| GluR-K2 \| HBGR2	glutamate receptor, ionotropic, AMPA 2	Reconstituted Complex	BioGRID	11891216
GRIA3	GLUR-C \| GLUR-K3 \| GLUR3 \| GLURC \| MRX94	glutamate receptor, ionotrophic, AMPA 3	Reconstituted Complex	BioGRID	11891216
GRIA4	GLUR4 \| GLUR4C \| GLURD	glutamate receptor, ionotrophic, AMPA 4	-	HPRD,BioGRID	11891216
GRIK1	EAA3 \| EEA3 \| GLR5 \| GLUR5	glutamate receptor, ionotropic, kainate 1	-	HPRD,BioGRID	12597860
GRIK2	EAA4 \| GLR6 \| GLUK6 \| GLUR6 \| MGC74427 \| MRT6	glutamate receptor, ionotropic, kainate 2	-	HPRD,BioGRID	12597860
GRIK3	EAA5 \| GLR7 \| GLUR7 \| GluR7a	glutamate receptor, ionotropic, kainate 3	Reconstituted Complex	BioGRID	11891216
GRM3	GLUR3 \| GPRC1C \| MGLUR3 \| mGlu3	glutamate receptor, metabotropic 3	-	HPRD,BioGRID	11891216
GRM7	FLJ40498 \| GLUR7 \| GPRC1G \| MGLUR7 \| mGlu7	glutamate receptor, metabotropic 7	Syntenin interacts with mGluR7b. This interaction was modeled on a demonstrated interaction between GRIP from an unspecified species and human mGluR7b.	BIND	11891216
IL5RA	CD125 \| CDw125 \| HSIL5R3 \| IL5R \| MGC26560	interleukin 5 receptor, alpha	-	HPRD,BioGRID	11498591
NF2	ACN \| BANF \| SCH	neurofibromin 2 (merlin)	Schwannomin interacts with syntenin.	BIND	11432873
NF2	ACN \| BANF \| SCH	neurofibromin 2 (merlin)	-	HPRD,BioGRID	11432873
NFASC	DKFZp686P2250 \| FLJ46866 \| KIAA0756 \| NF \| NRCAML	neurofascin homolog (chicken)	-	HPRD	11152476
NRXN1	DKFZp313P2036 \| FLJ35941 \| Hs.22998 \| KIAA0578	neurexin 1	Neurexin I-alpha interacts with ST-1. This interaction was modelled on a demonstrated interaction between human neurexin I-alpha and rat ST-1.	BIND	11152476
PTPRJ	CD148 \| DEP1 \| HPTPeta \| R-PTP-ETA \| SCC1	protein tyrosine phosphatase, receptor type, J	-	HPRD,BioGRID	12403354
RAB5A	RAB5	RAB5A, member RAS oncogene family	Affinity Capture-Western Two-hybrid	BioGRID	15014045
SDC1	CD138 \| SDC \| SYND1 \| syndecan	syndecan 1	-	HPRD,BioGRID	11179419
SDC2	HSPG \| HSPG1 \| SYND2	syndecan 2	-	HPRD,BioGRID	9391086
SDC3	N-syndecan \| SDCN \| SYND3	syndecan 3	Syndecan-3 interacts with ST-1. This interaction was modelled on a demonstrated interaction between human syndecan-3 and rat ST-1.	BIND	11152476
SDC4	MGC22217 \| SYND4	syndecan 4	-	HPRD	12241528
SDCBP2	FLJ12256 \| SITAC18 \| ST-2	syndecan binding protein (syntenin) 2	-	HPRD	11152476
SOX4	EVI16	SRY (sex determining region Y)-box 4	-	HPRD,BioGRID	11498591
TGFA	TFGA	transforming growth factor, alpha	Pro-TGF-alpha interacts with ST-1. This interaction was modelled on a demonstrated interaction between human Pro-TGF-alpha and rat ST-1.	BIND	11152476
ULK1	ATG1 \| FLJ38455 \| UNC51 \| Unc51.1	unc-51-like kinase 1 (C. elegans)	-	HPRD,BioGRID	15014045

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
PID IL5 PATHWAY	14	11	All SZGR 2.0 genes in this pathway
PID SYNDECAN 4 PATHWAY	32	25	All SZGR 2.0 genes in this pathway
PID SYNDECAN 1 PATHWAY	46	29	All SZGR 2.0 genes in this pathway
PID SYNDECAN 2 PATHWAY	33	27	All SZGR 2.0 genes in this pathway
REACTOME DEVELOPMENTAL BIOLOGY	396	292	All SZGR 2.0 genes in this pathway
REACTOME AXON GUIDANCE	251	188	All SZGR 2.0 genes in this pathway
REACTOME L1CAM INTERACTIONS	86	62	All SZGR 2.0 genes in this pathway
GARY CD5 TARGETS UP	473	314	All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP	1382	904	All SZGR 2.0 genes in this pathway
CHARAFE BREAST CANCER LUMINAL VS MESENCHYMAL DN	460	312	All SZGR 2.0 genes in this pathway
LAIHO COLORECTAL CANCER SERRATED UP	112	71	All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 2A DN	141	84	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
SCHLOSSER SERUM RESPONSE DN	712	443	All SZGR 2.0 genes in this pathway
FERREIRA EWINGS SARCOMA UNSTABLE VS STABLE UP	167	92	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 6HR UP	176	115	All SZGR 2.0 genes in this pathway
NIKOLSKY BREAST CANCER 8Q12 Q22 AMPLICON	132	82	All SZGR 2.0 genes in this pathway
DER IFN ALPHA RESPONSE UP	74	48	All SZGR 2.0 genes in this pathway
DORSAM HOXA9 TARGETS DN	32	22	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
DER IFN GAMMA RESPONSE UP	71	45	All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS MATURE CELL	293	160	All SZGR 2.0 genes in this pathway
WANG CISPLATIN RESPONSE AND XPC DN	228	146	All SZGR 2.0 genes in this pathway
JIANG HYPOXIA NORMAL	311	205	All SZGR 2.0 genes in this pathway
MARSON BOUND BY FOXP3 STIMULATED	1022	619	All SZGR 2.0 genes in this pathway
ZHENG FOXP3 TARGETS IN THYMUS UP	196	137	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
ALONSO METASTASIS EMT UP	36	24	All SZGR 2.0 genes in this pathway
ALONSO METASTASIS NEURAL UP	18	13	All SZGR 2.0 genes in this pathway
ALONSO METASTASIS UP	198	128	All SZGR 2.0 genes in this pathway
CROONQUIST NRAS SIGNALING UP	41	24	All SZGR 2.0 genes in this pathway
ROME INSULIN TARGETS IN MUSCLE UP	442	263	All SZGR 2.0 genes in this pathway
DANG REGULATED BY MYC DN	253	192	All SZGR 2.0 genes in this pathway
DORN ADENOVIRUS INFECTION 12HR DN	33	25	All SZGR 2.0 genes in this pathway
DORN ADENOVIRUS INFECTION 24HR DN	43	32	All SZGR 2.0 genes in this pathway
DORN ADENOVIRUS INFECTION 32HR DN	39	28	All SZGR 2.0 genes in this pathway
DORN ADENOVIRUS INFECTION 48HR DN	40	29	All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 9	76	45	All SZGR 2.0 genes in this pathway
LU EZH2 TARGETS DN	414	237	All SZGR 2.0 genes in this pathway
ALFANO MYC TARGETS	239	156	All SZGR 2.0 genes in this pathway
FORTSCHEGGER PHF8 TARGETS DN	784	464	All SZGR 2.0 genes in this pathway
PHONG TNF RESPONSE VIA P38 COMPLETE	227	151	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-1/206	497	503	1A	hsa-miR-1	UGGAAUGUAAAGAAGUAUGUA
				hsa-miR-206^SZ	UGGAAUGUAAGGAAGUGUGUGG
				hsa-miR-613	AGGAAUGUUCCUUCUUUGCC
miR-124.1	592	598	1A	hsa-miR-124a	UUAAGGCACGCGGUGAAUGCCA
miR-135	279	285	m8	hsa-miR-135a	UAUGGCUUUUUAUUCCUAUGUGA
miR-135	279	285	m8	hsa-miR-135b	UAUGGCUUUUCAUUCCUAUGUG
miR-142-5p	1036	1042	m8	hsa-miR-142-5p	CAUAAAGUAGAAAGCACUAC
miR-155	508	515	1A,m8	hsa-miR-155	UUAAUGCUAAUCGUGAUAGGGG
miR-17-5p/20/93.mr/106/519.d	1035	1041	1A	hsa-miR-17-5p	CAAAGUGCUUACAGUGCAGGUAGU
				hsa-miR-20a^brain	UAAAGUGCUUAUAGUGCAGGUAG
				hsa-miR-106a	AAAAGUGCUUACAGUGCAGGUAGC
				hsa-miR-106b^SZ	UAAAGUGCUGACAGUGCAGAU
				hsa-miR-20b^SZ	CAAAGUGCUCAUAGUGCAGGUAG
				hsa-miR-519d	CAAAGUGCCUCCCUUUAGAGUGU
miR-196	562	568	m8	hsa-miR-196a	UAGGUAGUUUCAUGUUGUUGG
miR-196	562	568	m8	hsa-miR-196b	UAGGUAGUUUCCUGUUGUUGG
miR-496	837	843	1A	hsa-miR-496	AUUACAUGGCCAAUCUC

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: SDCBP