SZGR2

Summary ?

GeneID	6382
Symbol	SDC1
Synonyms	CD138\|SDC\|SYND1\|syndecan
Description	syndecan 1
Reference	MIM:186355\|HGNC:HGNC:10658\|Ensembl:ENSG00000115884\|HPRD:01718\|Vega:OTTHUMG00000090751
Gene type	protein-coding
Map location	2p24.1
Pascal p-value	0.094
DEG p-value	DEG:Sanders_2014:DS1_p=-0.158:DS1_beta=0.026400:DS2_p=1.01e-03:DS2_beta=0.165:DS2_FDR=1.70e-02
Fetal beta	1.745
eGene	Myers' cis & trans

Gene in Data Sources

Gene set name	Method of gene set	Description
CV:GWAScat	Genome-wide Association Studies	This data set includes 560 SNPs associated with schizophrenia. A total of 486 genes were mapped to these SNPs within 50kb.
CV:PGCnp	Genome-wide Association Study	GWAS
DEG:Sanders_2013	Microarray	Whole-genome gene expression profiles using microarrays on lymphoblastoid cell lines (LCLs) from 413 cases and 446 controls.
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.008

Section I. Genetics and epigenetics annotation

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs10491487	chr5	80323367	SDC1	6382		0.09		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
NOL11	0.96	0.96
SMARCE1	0.96	0.96
CBX3	0.96	0.95
FAM76B	0.96	0.94
HNRNPH1	0.95	0.95
SMC3	0.95	0.93
CEP57	0.95	0.95
COIL	0.95	0.95
SNW1	0.95	0.96
DHX9	0.95	0.95

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
HLA-F	-0.73	-0.84
AIFM3	-0.71	-0.81
TSC22D4	-0.71	-0.85
AF347015.31	-0.70	-0.88
C5orf53	-0.70	-0.75
FXYD1	-0.70	-0.90
IFI27	-0.70	-0.90
MT-CO2	-0.69	-0.89
PTH1R	-0.69	-0.78
ALDOC	-0.69	-0.75

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0008092	cytoskeletal protein binding	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0016020	membrane	IEA		-
GO:0009986	cell surface	IEA		-
GO:0005887	integral to plasma membrane	TAS		2324102

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
CASK	CAGH39 \| CMG \| FLJ22219 \| FLJ31914 \| LIN2 \| MICPCH \| TNRC8	calcium/calmodulin-dependent serine protein kinase (MAGUK family)	-	HPRD,BioGRID	9660868
CCL5	D17S136E \| MGC17164 \| RANTES \| SCYA5 \| SISd \| TCP228	chemokine (C-C motif) ligand 5	-	HPRD,BioGRID	14637022
CTSG	CG \| MGC23078	cathepsin G	-	HPRD,BioGRID	9565572
ELA2	GE \| HLE \| HNE \| NE \| PMN-E	elastase 2, neutrophil	-	HPRD	9565572
FGF2	BFGF \| FGFB \| HBGF-2	fibroblast growth factor 2 (basic)	Co-purification	BioGRID	16982797
HGF	F-TCF \| HGFB \| HPTA \| SF	hepatocyte growth factor (hepapoietin A; scatter factor)	-	HPRD,BioGRID	11830493
IGFBP7	FSTL2 \| IGFBP-7 \| IGFBP-7v \| IGFBPRP1 \| MAC25 \| PSF	insulin-like growth factor binding protein 7	-	HPRD	14521955
IL8	CXCL8 \| GCP-1 \| GCP1 \| LECT \| LUCT \| LYNAP \| MDNCF \| MONAP \| NAF \| NAP-1 \| NAP1	interleukin 8	-	HPRD,BioGRID	12902511
LACRT	MGC71934	lacritin	Co-purification	BioGRID	16982797
MDK	FLJ27379 \| MK \| NEGF2	midkine (neurite growth-promoting factor 2)	-	HPRD	9089390
PTN	HARP \| HBGF8 \| HBNF \| NEGF1	pleiotrophin	-	HPRD	7592855
PTN	HARP \| HBGF8 \| HBNF \| NEGF1	pleiotrophin	Reconstituted Complex	BioGRID	8175719
SDCBP	MDA-9 \| ST1 \| SYCL \| TACIP18	syndecan binding protein (syntenin)	-	HPRD,BioGRID	11179419

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 INTEGRIN3 PATHWAY	43	25	All SZGR 2.0 genes in this pathway
PID AVB3 INTEGRIN PATHWAY	75	53	All SZGR 2.0 genes in this pathway
PID SYNDECAN 1 PATHWAY	46	29	All SZGR 2.0 genes in this pathway
PID INTEGRIN5 PATHWAY	17	9	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 LIPIDS AND LIPOPROTEINS	478	302	All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF CARBOHYDRATES	247	154	All SZGR 2.0 genes in this pathway
REACTOME LIPID DIGESTION MOBILIZATION AND TRANSPORT	46	37	All SZGR 2.0 genes in this pathway
REACTOME LIPOPROTEIN METABOLISM	28	24	All SZGR 2.0 genes in this pathway
REACTOME CHYLOMICRON MEDIATED LIPID TRANSPORT	16	15	All SZGR 2.0 genes in this pathway
NAKAMURA TUMOR ZONE PERIPHERAL VS CENTRAL DN	634	384	All SZGR 2.0 genes in this pathway
LIU PROSTATE CANCER DN	481	290	All SZGR 2.0 genes in this pathway
FRASOR TAMOXIFEN RESPONSE UP	51	36	All SZGR 2.0 genes in this pathway
DAVICIONI MOLECULAR ARMS VS ERMS DN	182	111	All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE LIVE DN	384	220	All SZGR 2.0 genes in this pathway
JAEGER METASTASIS DN	258	141	All SZGR 2.0 genes in this pathway
UDAYAKUMAR MED1 TARGETS UP	135	82	All SZGR 2.0 genes in this pathway
SENESE HDAC1 TARGETS DN	260	143	All SZGR 2.0 genes in this pathway
SENESE HDAC1 AND HDAC2 TARGETS DN	232	139	All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE FIMA DN	284	156	All SZGR 2.0 genes in this pathway
DELYS THYROID CANCER UP	443	294	All SZGR 2.0 genes in this pathway
CASTELLANO NRAS TARGETS UP	68	41	All SZGR 2.0 genes in this pathway
MARKEY RB1 CHRONIC LOF UP	115	78	All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN UP	1142	669	All SZGR 2.0 genes in this pathway
GRAESSMANN RESPONSE TO MC AND DOXORUBICIN UP	612	367	All SZGR 2.0 genes in this pathway
GAUSSMANN MLL AF4 FUSION TARGETS C UP	170	114	All SZGR 2.0 genes in this pathway
TAKADA GASTRIC CANCER COPY NUMBER UP	7	5	All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL BREAST 3 4WK UP	214	144	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 BREAST 6 7WK DN	79	54	All SZGR 2.0 genes in this pathway
MCBRYAN TERMINAL END BUD UP	12	12	All SZGR 2.0 genes in this pathway
LUND SILENCED BY METHYLATION	16	12	All SZGR 2.0 genes in this pathway
GRUETZMANN PANCREATIC CANCER UP	358	245	All SZGR 2.0 genes in this pathway
LI WILMS TUMOR VS FETAL KIDNEY 2 DN	51	42	All SZGR 2.0 genes in this pathway
HASINA NOL7 TARGETS DN	13	9	All SZGR 2.0 genes in this pathway
NUYTTEN NIPP1 TARGETS DN	848	527	All SZGR 2.0 genes in this pathway
INGRAM SHH TARGETS DN	64	41	All SZGR 2.0 genes in this pathway
WEI MYCN TARGETS WITH E BOX	795	478	All SZGR 2.0 genes in this pathway
RICKMAN TUMOR DIFFERENTIATED WELL VS POORLY DN	382	224	All SZGR 2.0 genes in this pathway
RICKMAN METASTASIS DN	261	155	All SZGR 2.0 genes in this pathway
PASQUALUCCI LYMPHOMA BY GC STAGE UP	283	177	All SZGR 2.0 genes in this pathway
BENPORATH CYCLING GENES	648	385	All SZGR 2.0 genes in this pathway
ONDER CDH1 TARGETS 2 DN	464	276	All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL AND BRAIN QTL TRANS	185	114	All SZGR 2.0 genes in this pathway
JECHLINGER EPITHELIAL TO MESENCHYMAL TRANSITION UP	71	51	All SZGR 2.0 genes in this pathway
IIZUKA LIVER CANCER PROGRESSION G2 G3 UP	28	14	All SZGR 2.0 genes in this pathway
TARTE PLASMA CELL VS PLASMABLAST UP	398	262	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
NING CHRONIC OBSTRUCTIVE PULMONARY DISEASE UP	157	105	All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS STEM CELL	254	164	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 48HR DN	504	323	All SZGR 2.0 genes in this pathway
GERHOLD ADIPOGENESIS DN	64	44	All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 2	72	52	All SZGR 2.0 genes in this pathway
SESTO RESPONSE TO UV C7	68	44	All SZGR 2.0 genes in this pathway
MAHAJAN RESPONSE TO IL1A UP	81	52	All SZGR 2.0 genes in this pathway
BILD HRAS ONCOGENIC SIGNATURE	261	166	All SZGR 2.0 genes in this pathway
DOUGLAS BMI1 TARGETS UP	566	371	All SZGR 2.0 genes in this pathway
ZHONG SECRETOME OF LUNG CANCER AND MACROPHAGE	77	50	All SZGR 2.0 genes in this pathway
CLASPER LYMPHATIC VESSELS DURING METASTASIS DN	36	23	All SZGR 2.0 genes in this pathway
MONNIER POSTRADIATION TUMOR ESCAPE UP	393	244	All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 5	482	296	All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS DN	292	189	All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS SILENCED BY METHYLATION DN	281	179	All SZGR 2.0 genes in this pathway
MASSARWEH TAMOXIFEN RESISTANCE UP	578	341	All SZGR 2.0 genes in this pathway
IWANAGA CARCINOGENESIS BY KRAS UP	170	107	All SZGR 2.0 genes in this pathway
PODAR RESPONSE TO ADAPHOSTIN DN	18	16	All SZGR 2.0 genes in this pathway
HUPER BREAST BASAL VS LUMINAL UP	54	29	All SZGR 2.0 genes in this pathway
BLUM RESPONSE TO SALIRASIB DN	342	220	All SZGR 2.0 genes in this pathway
GU PDEF TARGETS UP	71	49	All SZGR 2.0 genes in this pathway
CHANG CORE SERUM RESPONSE UP	212	128	All SZGR 2.0 genes in this pathway
CHANG CYCLING GENES	148	83	All SZGR 2.0 genes in this pathway
SWEET LUNG CANCER KRAS UP	491	316	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 HAPTOTAXIS DN	668	419	All SZGR 2.0 genes in this pathway
ROME INSULIN TARGETS IN MUSCLE DN	204	114	All SZGR 2.0 genes in this pathway
HOSHIDA LIVER CANCER SUBCLASS S3	266	180	All SZGR 2.0 genes in this pathway
WONG ADULT TISSUE STEM MODULE	721	492	All SZGR 2.0 genes in this pathway
WHITFIELD CELL CYCLE G1 S	147	76	All SZGR 2.0 genes in this pathway
PASINI SUZ12 TARGETS DN	315	215	All SZGR 2.0 genes in this pathway
TORCHIA TARGETS OF EWSR1 FLI1 FUSION DN	321	200	All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION DN	1080	713	All SZGR 2.0 genes in this pathway
SERVITJA ISLET HNF1A TARGETS UP	163	111	All SZGR 2.0 genes in this pathway
YANG BCL3 TARGETS UP	364	236	All SZGR 2.0 genes in this pathway
KRIEG HYPOXIA NOT VIA KDM3A	770	480	All SZGR 2.0 genes in this pathway
ALFANO MYC TARGETS	239	156	All SZGR 2.0 genes in this pathway
VANOEVELEN MYOGENESIS SIN3A TARGETS	220	133	All SZGR 2.0 genes in this pathway
SMIRNOV RESPONSE TO IR 6HR UP	166	97	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-10	750	757	1A,m8	hsa-miR-10a	UACCCUGUAGAUCCGAAUUUGUG
miR-10	750	757	1A,m8	hsa-miR-10b	UACCCUGUAGAACCGAAUUUGU
miR-19	510	517	1A,m8	hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
miR-19	510	517	1A,m8	hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
miR-28	1118	1124	m8	hsa-miR-28^brain	AAGGAGCUCACAGUCUAUUGAG
miR-9	1167	1173	1A	hsa-miR-9^SZ	UCUUUGGUUAUCUAGCUGUAUGA
miR-93.hd/291-3p/294/295/302/372/373/520	403	410	1A,m8	hsa-miR-93^brain	AAAGUGCUGUUCGUGCAGGUAG
				hsa-miR-302a	UAAGUGCUUCCAUGUUUUGGUGA
				hsa-miR-302b	UAAGUGCUUCCAUGUUUUAGUAG
				hsa-miR-302c	UAAGUGCUUCCAUGUUUCAGUGG
				hsa-miR-302d	UAAGUGCUUCCAUGUUUGAGUGU
				hsa-miR-372	AAAGUGCUGCGACAUUUGAGCGU
				hsa-miR-373	GAAGUGCUUCGAUUUUGGGGUGU
				hsa-miR-520e	AAAGUGCUUCCUUUUUGAGGG
				hsa-miR-520a	AAAGUGCUUCCCUUUGGACUGU
				hsa-miR-520b	AAAGUGCUUCCUUUUAGAGGG
				hsa-miR-520c	AAAGUGCUUCCUUUUAGAGGGUU
				hsa-miR-520d	AAAGUGCUUCUCUUUGGUGGGUU

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: SDC1