Gene Page:SNAPC1
Summary?
| GeneID | 6617 |
| Symbol | SNAPC1 |
| Synonyms | PTFgamma|SNAP43 |
| Description | small nuclear RNA activating complex polypeptide 1 |
| Reference | MIM:600591|HGNC:HGNC:11134|Ensembl:ENSG00000023608|HPRD:08998|Vega:OTTHUMG00000140343 |
| Gene type | protein-coding |
| Map location | 14q22 |
| Pascal p-value | 0.076 |
| Sherlock p-value | 0.539 |
| Fetal beta | -0.393 |
| 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: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. | 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 |
|---|---|---|---|---|---|---|---|
| cg22871002 | 14 | 62279623 | SNAPC1 | 4.66E-9 | -0.012 | 2.7E-6 | DMG:Jaffe_2016 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs3769467 | chr2 | 201205340 | SNAPC1 | 6617 | 0.01 | trans | ||
| rs3769461 | chr2 | 201222657 | SNAPC1 | 6617 | 0.01 | trans | ||
| rs1846982 | chr5 | 4431992 | SNAPC1 | 6617 | 0.19 | trans | ||
| snp_a-2169623 | 0 | SNAPC1 | 6617 | 0.03 | trans | |||
| rs7107326 | chr11 | 131332566 | SNAPC1 | 6617 | 0.03 | trans | ||
| rs16995131 | chr20 | 48844881 | SNAPC1 | 6617 | 0.15 | trans | ||
| rs407550 | chr21 | 46584075 | SNAPC1 | 6617 | 0.16 | 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
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 |
| SOX9 | 0.86 | 0.84 |
| PARD3 | 0.83 | 0.80 |
| KIF4A | 0.83 | 0.41 |
| SIX5 | 0.82 | 0.73 |
| NOTCH1 | 0.82 | 0.73 |
| NR2E1 | 0.81 | 0.81 |
| PALLD | 0.81 | 0.78 |
| CHST3 | 0.81 | 0.63 |
| NUSAP1 | 0.81 | 0.39 |
| CDC20 | 0.80 | 0.35 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| SLC26A4 | -0.28 | -0.36 |
| EPHX4 | -0.28 | -0.28 |
| FBXW7 | -0.28 | -0.29 |
| NPM2 | -0.27 | -0.20 |
| SERPINI1 | -0.27 | -0.26 |
| CA4 | -0.27 | -0.21 |
| C5orf53 | -0.27 | -0.22 |
| HTATIP2 | -0.26 | -0.16 |
| CHN1 | -0.26 | -0.12 |
| FABP3 | -0.26 | -0.22 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| REACTOME RNA POL III TRANSCRIPTION | 33 | 18 | All SZGR 2.0 genes in this pathway |
| REACTOME TRANSCRIPTION | 210 | 127 | All SZGR 2.0 genes in this pathway |
| REACTOME RNA POL I RNA POL III AND MITOCHONDRIAL TRANSCRIPTION | 122 | 80 | All SZGR 2.0 genes in this pathway |
| REACTOME RNA POL III TRANSCRIPTION INITIATION FROM TYPE 3 PROMOTER | 26 | 13 | All SZGR 2.0 genes in this pathway |
| SENESE HDAC3 TARGETS DN | 536 | 332 | All SZGR 2.0 genes in this pathway |
| KIM WT1 TARGETS DN | 459 | 276 | All SZGR 2.0 genes in this pathway |
| RODRIGUES THYROID CARCINOMA POORLY DIFFERENTIATED UP | 633 | 376 | All SZGR 2.0 genes in this pathway |
| ENK UV RESPONSE KERATINOCYTE UP | 530 | 342 | All SZGR 2.0 genes in this pathway |
| LINDGREN BLADDER CANCER CLUSTER 1 UP | 121 | 71 | All SZGR 2.0 genes in this pathway |
| HAMAI APOPTOSIS VIA TRAIL UP | 584 | 356 | All SZGR 2.0 genes in this pathway |
| SCHLOSSER SERUM RESPONSE DN | 712 | 443 | All SZGR 2.0 genes in this pathway |
| PUJANA BRCA1 PCC NETWORK | 1652 | 1023 | All SZGR 2.0 genes in this pathway |
| NUYTTEN NIPP1 TARGETS DN | 848 | 527 | All SZGR 2.0 genes in this pathway |
| ROPERO HDAC2 TARGETS | 114 | 71 | All SZGR 2.0 genes in this pathway |
| BENPORATH SOX2 TARGETS | 734 | 436 | All SZGR 2.0 genes in this pathway |
| BENPORATH MYC MAX TARGETS | 775 | 494 | All SZGR 2.0 genes in this pathway |
| DEBIASI APOPTOSIS BY REOVIRUS INFECTION UP | 314 | 201 | All SZGR 2.0 genes in this pathway |
| BANDRES RESPONSE TO CARMUSTIN WITHOUT MGMT 24HR UP | 14 | 10 | All SZGR 2.0 genes in this pathway |
| BLALOCK ALZHEIMERS DISEASE UP | 1691 | 1088 | All SZGR 2.0 genes in this pathway |
| BROWNE HCMV INFECTION 48HR UP | 180 | 125 | 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 |
| IVANOVA HEMATOPOIESIS STEM CELL AND PROGENITOR | 681 | 420 | All SZGR 2.0 genes in this pathway |
| BANDRES RESPONSE TO CARMUSTIN MGMT 48HR UP | 18 | 13 | All SZGR 2.0 genes in this pathway |
| MCCABE BOUND BY HOXC6 | 469 | 239 | All SZGR 2.0 genes in this pathway |
| AGUIRRE PANCREATIC CANCER COPY NUMBER UP | 298 | 174 | All SZGR 2.0 genes in this pathway |
| DANG BOUND BY MYC | 1103 | 714 | All SZGR 2.0 genes in this pathway |
| BANDRES RESPONSE TO CARMUSTIN MGMT 24HR UP | 9 | 5 | All SZGR 2.0 genes in this pathway |
| HIRSCH CELLULAR TRANSFORMATION SIGNATURE UP | 242 | 159 | All SZGR 2.0 genes in this pathway |
| BRUINS UVC RESPONSE VIA TP53 GROUP D | 280 | 158 | All SZGR 2.0 genes in this pathway |
| ZWANG CLASS 1 TRANSIENTLY INDUCED BY EGF | 516 | 308 | All SZGR 2.0 genes in this pathway |