Gene Page:SH2D3C
Summary?
| GeneID | 10044 |
| Symbol | SH2D3C |
| Synonyms | CHAT|NSP3|PRO34088|SHEP1 |
| Description | SH2 domain containing 3C |
| Reference | MIM:604722|HGNC:HGNC:16884|Ensembl:ENSG00000095370|HPRD:05284|Vega:OTTHUMG00000020717 |
| Gene type | protein-coding |
| Map location | 9q34.11 |
| Pascal p-value | 0.19 |
| Sherlock p-value | 0.828 |
| Fetal beta | -0.305 |
| DMG | 1 (# studies) |
| eGene | Cortex Myers' cis & trans |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:PGCnp | Genome-wide Association Study | GWAS | |
| DMG:vanEijk_2014 | Genome-wide DNA methylation analysis | This dataset includes 432 differentially methylated CpG sites corresponding to 391 unique transcripts between schizophrenia patients (n=260) and unaffected controls (n=250). | 1 |
Section I. Genetics and epigenetics annotation
Differentially methylated gene
Differentially methylated gene| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg24910675 | 9 | 130616917 | SH2D3C | 6.965E-4 | -4.551 | DMG:vanEijk_2014 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs4497566 | chr13 | 51694324 | SH2D3C | 10044 | 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 |
| MRPL1 | 0.90 | 0.90 |
| RG9MTD1 | 0.88 | 0.89 |
| ACTR6 | 0.88 | 0.90 |
| VPS29 | 0.88 | 0.87 |
| SUB1 | 0.88 | 0.89 |
| PSMC6 | 0.87 | 0.88 |
| NFU1 | 0.87 | 0.89 |
| CHMP5 | 0.87 | 0.85 |
| CAPZA2 | 0.87 | 0.85 |
| ATP5C1 | 0.85 | 0.86 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| FAM38A | -0.57 | -0.62 |
| AF347015.26 | -0.56 | -0.54 |
| AF347015.15 | -0.55 | -0.52 |
| AF347015.2 | -0.55 | -0.51 |
| AF347015.8 | -0.54 | -0.50 |
| MT-CYB | -0.53 | -0.50 |
| TENC1 | -0.53 | -0.54 |
| GPT | -0.52 | -0.55 |
| PPP1R13L | -0.52 | -0.53 |
| AF347015.33 | -0.52 | -0.50 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| GARGALOVIC RESPONSE TO OXIDIZED PHOSPHOLIPIDS GREY DN | 74 | 44 | 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 |
| AMUNDSON RESPONSE TO ARSENITE | 217 | 143 | All SZGR 2.0 genes in this pathway |
| SUH COEXPRESSED WITH ID1 AND ID2 UP | 19 | 14 | All SZGR 2.0 genes in this pathway |
| BENPORATH MYC MAX TARGETS | 775 | 494 | All SZGR 2.0 genes in this pathway |
| HADDAD B LYMPHOCYTE PROGENITOR | 293 | 193 | All SZGR 2.0 genes in this pathway |
| MA MYELOID DIFFERENTIATION UP | 39 | 29 | All SZGR 2.0 genes in this pathway |
| MARSON BOUND BY FOXP3 UNSTIMULATED | 1229 | 713 | All SZGR 2.0 genes in this pathway |
| 拉贝风TGFB1目标S DN | 108 | 64 | All SZGR 2.0 genes in this pathway |
| ROME INSULIN TARGETS IN MUSCLE DN | 204 | 114 | All SZGR 2.0 genes in this pathway |
| DANG BOUND BY MYC | 1103 | 714 | All SZGR 2.0 genes in this pathway |