Gene Page:SDC2

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 pvalue qvalue TSS distance 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)

Not available

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
死神:胎儿(13 - 26 postconception周),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 去的术语 Evidence Neuro keywords PubMed ID
GO:0003674 molecular_function ND -
GO:0008092 cytoskeletal protein binding IEA -
Biological process 去的术语 Evidence Neuro keywords PubMed ID
GO:0008150 biological_process ND -
Cellular component 去的术语 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附属 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
UTR start UTR end Match method
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-218brain UUGUGCUUGAUCUAACCAUGU
miR-25/32/92/363/367 465 471 m8 hsa-miR-25brain CAUUGCACUUGUCUCGGUCUGA
hsa-miR-32 UAUUGCACAUUACUAAGUUGC
hsa-miR-92 UAUUGCACUUGUCCCGGCCUG
hsa-miR-367 AAUUGCACUUUAGCAAUGGUGA
hsa-miR-92bSZ UAUUGCACUCGUCCCGGCCUC
miR-27 201 207 1A hsa-miR-27abrain UUCACAGUGGCUAAGUUCCGC
hsa-miR-27bbrain 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-9SZ UCUUUGGUUAUCUAGCUGUAUGA
hsa-miR-9SZ UCUUUGGUUAUCUAGCUGUAUGA
miR-96 2191 2198 1A,m8 hsa-miR-96brain UUUGGCACUAGCACAUUUUUGC