SZGR2

Summary ?

GeneID	6383
Symbol	SDC2
Synonyms	CD362\|HSPG\|HSPG1\|SYND2
Description	syndecan 2
Reference	MIM:142460\|HGNC:HGNC:10659\|Ensembl:ENSG00000169439\|HPRD:00803\|Vega:OTTHUMG00000164689
Gene type	protein-coding
Map location	8q22-q23
Pascal p-value	0.038
Fetal beta	-1.198
DMG	2 (# studies)
eGene	Myers' cis & trans

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:GWASdb	Genome-wide Association Studies	GWASdb records for schizophrenia
CV:PGCnp	Genome-wide Association Study	GWAS
DMG:Jaffe_2016	Genome-wide DNA methylation analysis	This dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05.	2
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.	2
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.0329

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg14538332	8	97506180	SDC2		-0.025	0.37	DMG:Nishioka_2013
cg16673702	8	97507592	SDC2	7.79E-8	-0.01	1.84E-5	DMG:Jaffe_2016

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs9882137	chr3	29494146	SDC2	6383	0.01	trans
rs9882501	chr3	29494429	SDC2	6383	0.07	trans
snp_a-1789759		0	SDC2	6383	0.14	trans
rs17139868	chr7	117079228	SDC2	6383	0.01	trans

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
ZNF416	0.92	0.88
PRPSAP2	0.92	0.89
WDR70	0.92	0.90
BZW2	0.91	0.92
ZNF555	0.91	0.85
RFWD2	0.91	0.90
YTHDF2	0.91	0.84
C12orf41	0.91	0.90
EIF4A1	0.90	0.90
ZNF259	0.90	0.87

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AF347015.33	-0.73	-0.87
AF347015.27	-0.72	-0.84
MT-CO2	-0.72	-0.83
MT-CYB	-0.72	-0.86
AF347015.31	-0.72	-0.83
AIFM3	-0.71	-0.79
AF347015.8	-0.70	-0.85
HLA-F	-0.70	-0.76
HEPN1	-0.70	-0.77
AF347015.15	-0.70	-0.85

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0003674	molecular_function	ND		-
GO:0008092	cytoskeletal protein binding	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0008150	biological_process	ND		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0016020	membrane	IEA		-
GO:0005887	integral to plasma membrane	NAS		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
APOE	AD2 \| LPG \| MGC1571 \| apoprotein	apolipoprotein E	-	HPRD	9869645
CASK	CAGH39 \| CMG \| FLJ22219 \| FLJ31914 \| LIN2 \| MICPCH \| TNRC8	calcium/calmodulin-dependent serine protein kinase (MAGUK family)	-	HPRD,BioGRID	9660868
CSF2	GMCSF \| MGC131935 \| MGC138897	colony stimulating factor 2 (granulocyte-macrophage)	-	HPRD,BioGRID	10734053
CSF2RA	CD116 \| CDw116 \| CSF2R \| CSF2RAX \| CSF2RAY \| CSF2RX \| CSF2RY \| GM-CSF-R-alpha \| GMCSFR \| GMR \| MGC3848 \| MGC4838	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	Affinity Capture-Western	BioGRID	10734053
EPB41L1	4.1N \| DKFZp686H17242 \| KIAA0338 \| MGC11072	erythrocyte membrane protein band 4.1-like 1	Affinity Capture-Western	BioGRID	12676536
EZR	CVIL \| CVL \| DKFZp762H157 \| FLJ26216 \| MGC1584 \| VIL2	ezrin	-	HPRD,BioGRID	10704377
FGF2	BFGF \| FGFB \| HBGF-2	fibroblast growth factor 2 (basic)	Co-purification	BioGRID	16982797
FN1	CIG \| DKFZp686F10164 \| DKFZp686H0342 \| DKFZp686I1370 \| DKFZp686O13149 \| ED-B \| FINC \| FN \| FNZ \| GFND \| GFND2 \| LETS \| MSF	fibronectin 1	-	HPRD,BioGRID	10772816
HGF	F-TCF \| HGFB \| HPTA \| SF	hepatocyte growth factor (hepapoietin A; scatter factor)	-	HPRD,BioGRID	8157651
ITPR1	INSP3R1 \| IP3R \| IP3R1 \| SCA15 \| SCA16	inositol 1,4,5-triphosphate receptor, type 1	Affinity Capture-Western	BioGRID	12676536
KAL1	ADMLX \| HHA \| KAL \| KALIG-1 \| KMS	Kallmann syndrome 1 sequence	-	HPRD,BioGRID	8832397
LAMA3	BM600 \| E170 \| LAMNA \| LOCS \| lama3a	laminin, alpha 3	-	HPRD,BioGRID	11373281
PF4	CXCL4 \| MGC138298 \| SCYB4	platelet factor 4	-	HPRD,BioGRID	7524669
REG3A	HIP \| INGAP \| PAP \| PAP-H \| PAP1 \| PBCGF \| REG-III \| REG3	regenerating islet-derived 3 alpha	-	HPRD,BioGRID	8997243
SDCBP	MDA-9 \| ST1 \| SYCL \| TACIP18	syndecan binding protein (syntenin)	-	HPRD,BioGRID	9391086
SERPINC1	AT3 \| ATIII \| MGC22579	serpin peptidase inhibitor, clade C (antithrombin), member 1	-	HPRD	1315572
SPARC	ON	secreted protein, acidic, cysteine-rich (osteonectin)	-	HPRD	2745554
TRAPPC4	CGI-104 \| HSPC172 \| PTD009 \| SBDN \| SYNBINDIN \| TRS23	trafficking protein particle complex 4	-	HPRD	11018053

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG ECM RECEPTOR INTERACTION	84	53	All SZGR 2.0 genes in this pathway
KEGG CELL ADHESION MOLECULES CAMS	134	93	All SZGR 2.0 genes in this pathway
PID SHP2 PATHWAY	58	46	All SZGR 2.0 genes in this pathway
PID SYNDECAN 2 PATHWAY	33	27	All SZGR 2.0 genes in this pathway
PID FGF PATHWAY	55	37	All SZGR 2.0 genes in this pathway
REACTOME HS GAG DEGRADATION	20	15	All SZGR 2.0 genes in this pathway
REACTOME CHONDROITIN SULFATE DERMATAN SULFATE METABOLISM	49	33	All SZGR 2.0 genes in this pathway
REACTOME HS GAG BIOSYNTHESIS	31	17	All SZGR 2.0 genes in this pathway
REACTOME HEPARAN SULFATE HEPARIN HS GAG METABOLISM	52	33	All SZGR 2.0 genes in this pathway
REACTOME GLYCOSAMINOGLYCAN METABOLISM	111	69	All SZGR 2.0 genes in this pathway
REACTOME A TETRASACCHARIDE LINKER SEQUENCE IS REQUIRED FOR GAG SYNTHESIS	25	17	All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF CARBOHYDRATES	247	154	All SZGR 2.0 genes in this pathway
SCHUETZ BREAST CANCER DUCTAL INVASIVE UP	351	230	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
FULCHER INFLAMMATORY RESPONSE LECTIN VS LPS UP	579	346	All SZGR 2.0 genes in this pathway
THUM SYSTOLIC HEART FAILURE UP	423	283	All SZGR 2.0 genes in this pathway
TONKS TARGETS OF RUNX1 RUNX1T1 FUSION MONOCYTE DN	54	38	All SZGR 2.0 genes in this pathway
SENESE HDAC1 AND HDAC2 TARGETS DN	232	139	All SZGR 2.0 genes in this pathway
SENESE HDAC2 TARGETS DN	133	77	All SZGR 2.0 genes in this pathway
SENESE HDAC3 TARGETS DN	536	332	All SZGR 2.0 genes in this pathway
WAMUNYOKOLI OVARIAN CANCER LMP DN	199	124	All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA DN	1375	806	All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA POORLY DIFFERENTIATED DN	805	505	All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA ANAPLASTIC DN	537	339	All SZGR 2.0 genes in this pathway
DELYS THYROID CANCER DN	232	154	All SZGR 2.0 genes in this pathway
HERNANDEZ MITOTIC ARREST BY DOCETAXEL 1 DN	38	23	All SZGR 2.0 genes in this pathway
SASAI RESISTANCE TO NEOPLASTIC TRANSFROMATION	50	31	All SZGR 2.0 genes in this pathway
HASINA NOL7 TARGETS DN	13	9	All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS DN	637	377	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 48HR DN	428	306	All SZGR 2.0 genes in this pathway
BALDWIN PRKCI TARGETS UP	35	26	All SZGR 2.0 genes in this pathway
BENPORATH SUZ12 TARGETS	1038	678	All SZGR 2.0 genes in this pathway
BENPORATH EED TARGETS	1062	725	All SZGR 2.0 genes in this pathway
WANG PROSTATE CANCER ANDROGEN INDEPENDENT	66	37	All SZGR 2.0 genes in this pathway
NIKOLSKY BREAST CANCER 8Q12 Q22 AMPLICON	132	82	All SZGR 2.0 genes in this pathway
ONDER CDH1 TARGETS 2 UP	256	159	All SZGR 2.0 genes in this pathway
JECHLINGER EPITHELIAL TO MESENCHYMAL TRANSITION UP	71	51	All SZGR 2.0 genes in this pathway
FRASOR RESPONSE TO ESTRADIOL UP	37	28	All SZGR 2.0 genes in this pathway
SMITH LIVER CANCER	45	27	All SZGR 2.0 genes in this pathway
LENAOUR DENDRITIC CELL MATURATION DN	128	90	All SZGR 2.0 genes in this pathway
ZHAN MULTIPLE MYELOMA CD2 UP	45	32	All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 DN	830	547	All SZGR 2.0 genes in this pathway
DELASERNA MYOD TARGETS DN	57	42	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 48HR DN	504	323	All SZGR 2.0 genes in this pathway
LU AGING BRAIN UP	262	186	All SZGR 2.0 genes in this pathway
TSENG IRS1 TARGETS UP	113	71	All SZGR 2.0 genes in this pathway
BAELDE DIABETIC NEPHROPATHY DN	434	302	All SZGR 2.0 genes in this pathway
WANG SMARCE1 TARGETS UP	280	183	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 12HR DN	101	64	All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 6HR DN	911	527	All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 24HR UP	783	442	All SZGR 2.0 genes in this pathway
CLASPER LYMPHATIC VESSELS DURING METASTASIS DN	36	23	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
SMID BREAST CANCER BASAL UP	648	398	All SZGR 2.0 genes in this pathway
BONOME OVARIAN CANCER SURVIVAL SUBOPTIMAL DEBULKING	510	309	All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL UP	260	174	All SZGR 2.0 genes in this pathway
RAY TUMORIGENESIS BY ERBB2 CDC25A DN	159	105	All SZGR 2.0 genes in this pathway
GU PDEF TARGETS UP	71	49	All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS DN	366	257	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
HAN SATB1 TARGETS DN	442	275	All SZGR 2.0 genes in this pathway
CHEN METABOLIC SYNDROM NETWORK	1210	725	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 4HR DN	254	158	All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS UP	504	321	All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP A	898	516	All SZGR 2.0 genes in this pathway
FEVR CTNNB1 TARGETS DN	553	343	All SZGR 2.0 genes in this pathway
WINZEN DEGRADED VIA KHSRP	100	70	All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION DN	1080	713	All SZGR 2.0 genes in this pathway
PEDERSEN METASTASIS BY ERBB2 ISOFORM 7	403	240	All SZGR 2.0 genes in this pathway
NABA ECM AFFILIATED	171	89	All SZGR 2.0 genes in this pathway
NABA MATRISOME ASSOCIATED	753	411	All SZGR 2.0 genes in this pathway
NABA MATRISOME	1028	559	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-124.1	1928	1934	1A	hsa-miR-124a	UUAAGGCACGCGGUGAAUGCCA
miR-182	2192	2198	1A	hsa-miR-182	UUUGGCAAUGGUAGAACUCACA
miR-186	157	163	1A	hsa-miR-186	CAAAGAAUUCUCCUUUUGGGCUU
miR-200bc/429	757	763	m8	hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
miR-218	988	994	m8	hsa-miR-218^brain	UUGUGCUUGAUCUAACCAUGU
miR-25/32/92/363/367	465	471	m8	hsa-miR-25^brain	CAUUGCACUUGUCUCGGUCUGA
				hsa-miR-32	UAUUGCACAUUACUAAGUUGC
				hsa-miR-92	UAUUGCACUUGUCCCGGCCUG
				hsa-miR-367	AAUUGCACUUUAGCAAUGGUGA
				hsa-miR-92b^SZ	UAUUGCACUCGUCCCGGCCUC
miR-27	201	207	1A	hsa-miR-27a^brain	UUCACAGUGGCUAAGUUCCGC
miR-27	201	207	1A	hsa-miR-27b^brain	UUCACAGUGGCUAAGUUCUGC
miR-376c	917	924	1A,m8	hsa-miR-376c	AACAUAGAGGAAAUUCCACG
miR-485-5p	731	737	1A	hsa-miR-485-5p	AGAGGCUGGCCGUGAUGAAUUC
miR-493-5p	1131	1137	m8	hsa-miR-493-5p	UUGUACAUGGUAGGCUUUCAUU
miR-499	1019	1025	m8	hsa-miR-499	UUAAGACUUGCAGUGAUGUUUAA
miR-500	464	470	1A	hsa-miR-500	AUGCACCUGGGCAAGGAUUCUG
miR-9	1428	1434	1A	hsa-miR-9^SZ	UCUUUGGUUAUCUAGCUGUAUGA
miR-9	1428	1434	1A	hsa-miR-9^SZ	UCUUUGGUUAUCUAGCUGUAUGA
miR-96	2191	2198	1A,m8	hsa-miR-96^brain	UUUGGCACUAGCACAUUUUUGC

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: SDC2