Gene Page: SNCG
Summary ?
| GeneID | 6623 |
| Symbol | SNCG |
| Synonyms | BCSG1|SR |
| Description | synuclein gamma |
| Reference | MIM:602998|HGNC:HGNC:11141|Ensembl:ENSG00000173267|HPRD:04297|Vega:OTTHUMG00000018656 |
| Gene type | protein-coding |
| Map location | 10q23.2-q23.3 |
| Pascal p-value | 0.788 |
| Sherlock p-value | 0.092 |
| Fetal beta | -2.45 |
| DMG | 1 (# studies) |
| eGene | Myers' cis & trans |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:PGCnp | Genome-wide Association Study | GWAS | |
| DMG:Wockner_2014 | Genome-wide DNA methylation analysis | This dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24). | 1 |
| GO_Annotation | Mapping neuro-related keywords to Gene Ontology annotations | Hits with neuro-related keywords: 2 |
Section I. Genetics and epigenetics annotation
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg10414829 | 10 | 88719259 | SNCG | 6.96E-5 | 0.278 | 0.024 | DMG:Wockner_2014 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs4655259 | chr1 | 214637099 | SNCG | 6623 | 0.15 | 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 |
| EFHD1 | 0.94 | 0.91 |
| PRR18 | 0.93 | 0.93 |
| CNP | 0.93 | 0.91 |
| HSPA2 | 0.91 | 0.89 |
| FA2H | 0.90 | 0.91 |
| CLDN11 | 0.90 | 0.83 |
| ZCCHC24 | 0.89 | 0.91 |
| ERBB3 | 0.89 | 0.94 |
| MAG | 0.89 | 0.88 |
| PADI2 | 0.89 | 0.91 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| POLB | -0.61 | -0.74 |
| TRNAU1AP | -0.60 | -0.68 |
| NR2C2AP | -0.60 | -0.71 |
| STMN1 | -0.59 | -0.67 |
| ING4 | -0.59 | -0.66 |
| DUSP12 | -0.58 | -0.66 |
| MED19 | -0.58 | -0.67 |
| HN1 | -0.58 | -0.65 |
| ALKBH2 | -0.58 | -0.71 |
| NKIRAS2 | -0.58 | -0.57 |
Section III. Gene Ontology annotation
| Molecular function | GO term | Evidence | Neuro keywords | PubMed ID |
|---|---|---|---|---|
| GO:0005515 | protein binding | IPI | 17353931 | |
| Cellular component | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0043025 | cell soma | IEA | axon, dendrite (GO term level: 4) | - |
| GO:0030424 | axon | IEA | neuron, axon, Neurotransmitter (GO term level: 6) | - |
| GO:0005813 | centrosome | IEA | - | |
| GO:0005819 | spindle | IEA | - | |
| GO:0005737 | cytoplasm | IEA | - |
Section IV. Protein-protein interaction annotation
| Interactors | Aliases B | Official full name B | Experimental | Source | PubMed ID |
|---|---|---|---|---|---|
| BUB1B | BUB1beta | BUBR1 | Bub1A | MAD3L | SSK1 | hBUBR1 | budding uninhibited by benzimidazoles 1 homolog beta (yeast) | - | HPRD,BioGRID | 14576821 |
| DYNLL1 | DLC1 | DLC8 | DNCL1 | DNCLC1 | LC8 | LC8a | MGC126137 | MGC126138 | PIN | hdlc1 | dynein, light chain, LC8-type 1 | Affinity Capture-MS | BioGRID | 17353931 |
| EXT2 | SOTV | exostoses (multiple) 2 | Affinity Capture-MS | BioGRID | 17353931 |
| FABP4 | A-FABP | aP2 | fatty acid binding protein 4, adipocyte | Affinity Capture-MS | BioGRID | 17353931 |
| FUBP1 | FBP | FUBP | far upstream element (FUSE) binding protein 1 | Affinity Capture-MS | BioGRID | 17353931 |
| GRK1 | GPRK1 | RHOK | RK | G protein-coupled receptor kinase 1 | Biochemical Activity | BioGRID | 10852916 |
| GRK5 | GPRK5 | G protein-coupled receptor kinase 5 | - | HPRD,BioGRID | 10852916 |
| GRK6 | FLJ32135 | GPRK6 | G protein-coupled receptor kinase 6 | Biochemical Activity | BioGRID | 10852916 |
| HNF4A | FLJ39654 | HNF4 | HNF4a7 | HNF4a8 | HNF4a9 | MODY | MODY1 | NR2A1 | NR2A21 | TCF | TCF14 | hepatocyte nuclear factor 4, alpha | Affinity Capture-MS | BioGRID | 17353931 |
| MAPK1 | ERK | ERK2 | ERT1 | MAPK2 | P42MAPK | PRKM1 | PRKM2 | p38 | p40 | p41 | p41mapk | mitogen-activated protein kinase 1 | Affinity Capture-Western | BioGRID | 12121974 |
| MAPK3 | ERK1 | HS44KDAP | HUMKER1A | MGC20180 | P44ERK1 | P44MAPK | PRKM3 | mitogen-activated protein kinase 3 | Affinity Capture-Western | BioGRID | 12121974 |
| MAPK8 | JNK | JNK1 | JNK1A2 | JNK21B1/2 | PRKM8 | SAPK1 | mitogen-activated protein kinase 8 | - | HPRD,BioGRID | 12121974 |
| MCM3 | HCC5 | MGC1157 | P1-MCM3 | P1.h | RLFB | minichromosome maintenance complex component 3 | Affinity Capture-MS | BioGRID | 17353931 |
| TIMP2 | CSC-21K | TIMP metallopeptidase inhibitor 2 | Affinity Capture-MS | BioGRID | 17353931 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| LINDGREN BLADDER CANCER CLUSTER 2A UP | 8 | 5 | 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 |
| MCBRYAN PUBERTAL BREAST 6 7WK UP | 197 | 135 | All SZGR 2.0 genes in this pathway |
| LOPEZ MBD TARGETS | 957 | 597 | All SZGR 2.0 genes in this pathway |
| GOUYER TATI TARGETS DN | 17 | 12 | All SZGR 2.0 genes in this pathway |
| LE EGR2 TARGETS DN | 108 | 84 | All SZGR 2.0 genes in this pathway |
| FRASOR RESPONSE TO ESTRADIOL DN | 82 | 52 | All SZGR 2.0 genes in this pathway |
| BLALOCK ALZHEIMERS DISEASE DN | 1237 | 837 | All SZGR 2.0 genes in this pathway |
| BANDRES RESPONSE TO CARMUSTIN WITHOUT MGMT 48HR UP | 18 | 13 | All SZGR 2.0 genes in this pathway |
| XU GH1 AUTOCRINE TARGETS UP | 268 | 157 | All SZGR 2.0 genes in this pathway |
| MARTINEZ RB1 TARGETS UP | 673 | 430 | All SZGR 2.0 genes in this pathway |
| MARTINEZ TP53 TARGETS UP | 602 | 364 | All SZGR 2.0 genes in this pathway |
| MARTINEZ RB1 AND TP53 TARGETS UP | 601 | 369 | All SZGR 2.0 genes in this pathway |
| SMID BREAST CANCER BASAL DN | 701 | 446 | All SZGR 2.0 genes in this pathway |
| RAY TUMORIGENESIS BY ERBB2 CDC25A DN | 159 | 105 | All SZGR 2.0 genes in this pathway |
| YOSHIMURA MAPK8 TARGETS UP | 1305 | 895 | All SZGR 2.0 genes in this pathway |
| SHEDDEN LUNG CANCER POOR SURVIVAL A6 | 456 | 285 | All SZGR 2.0 genes in this pathway |
| VERHAAK GLIOBLASTOMA NEURAL | 129 | 85 | All SZGR 2.0 genes in this pathway |
| LU EZH2 TARGETS UP | 295 | 155 | All SZGR 2.0 genes in this pathway |
| ACOSTA PROLIFERATION INDEPENDENT MYC TARGETS DN | 116 | 74 | All SZGR 2.0 genes in this pathway |
| KATSANOU ELAVL1 TARGETS UP | 169 | 105 | All SZGR 2.0 genes in this pathway |
| SERVITJA ISLET HNF1A TARGETS UP | 163 | 111 | All SZGR 2.0 genes in this pathway |
| WAKABAYASHI ADIPOGENESIS PPARG RXRA BOUND 36HR | 152 | 88 | All SZGR 2.0 genes in this pathway |
| WAKABAYASHI ADIPOGENESIS PPARG RXRA BOUND 8D | 882 | 506 | All SZGR 2.0 genes in this pathway |
| PLASARI TGFB1 SIGNALING VIA NFIC 1HR DN | 106 | 77 | All SZGR 2.0 genes in this pathway |
| ZWANG TRANSIENTLY UP BY 1ST EGF PULSE ONLY | 1839 | 928 | All SZGR 2.0 genes in this pathway |