Gene Page: TRANK1
Summary ?
| GeneID | 9881 |
| Symbol | TRANK1 |
| Synonyms | LBA1 |
| Description | tetratricopeptide repeat and ankyrin repeat containing 1 |
| Reference | HGNC:HGNC:29011|Ensembl:ENSG00000168016|Vega:OTTHUMG00000155848 |
| Gene type | protein-coding |
| Map location | 3p22.2 |
| Pascal p-value | 3.587E-9 |
| Sherlock p-value | 0.591 |
| Fetal beta | -0.518 |
| DMG | 1 (# studies) |
| eGene | Myers' cis & trans |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| 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:GWASdb | Genome-wide Association Studies | GWASdb records for schizophrenia | |
| CV:PGC128 | Genome-wide Association Study | A multi-stage schizophrenia GWAS of up to 36,989 cases and 113,075 controls. Reported by the Schizophrenia Working Group of PGC. 128 independent associations spanning 108 loci | |
| 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 |
| PMID:cooccur | High-throughput literature-search | Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included. | |
| Literature | High-throughput literature-search | Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophrenias | Click to show details |
Section I. Genetics and epigenetics annotation
CV:PGC128
| SNP ID | Chromosome | Position | Allele | P | Function | Gene | Up/Down Distance |
|---|---|---|---|---|---|---|---|
| rs75968099 | chr3 | 36858583 | TC | 3.386E-12 | intergenic | DCLK3,TRANK1 | dist=77231;dist=9725 |
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg01349853 | 3 | 36986697 | TRANK1 | 5.71E-8 | -0.012 | 1.46E-5 | DMG:Jaffe_2016 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs16829545 | chr2 | 151977407 | TRANK1 | 9881 | 0.01 | trans | ||
| rs3845734 | chr2 | 171125572 | TRANK1 | 9881 | 0.11 | trans | ||
| rs7584986 | chr2 | 184111432 | TRANK1 | 9881 | 0.03 | trans | ||
| rs7036187 | chr9 | 88602015 | TRANK1 | 9881 | 0.04 | trans | ||
| rs16955618 | chr15 | 29937543 | TRANK1 | 9881 | 4.999E-5 | 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 |
| SGTA | 0.93 | 0.94 |
| MANEAL | 0.93 | 0.93 |
| ZNF574 | 0.93 | 0.92 |
| COBRA1 | 0.92 | 0.93 |
| TOR2A | 0.92 | 0.91 |
| SIGMAR1 | 0.92 | 0.91 |
| FZR1 | 0.92 | 0.94 |
| MEN1 | 0.92 | 0.93 |
| GPR172A | 0.92 | 0.92 |
| SCAP | 0.92 | 0.92 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| AF347015.31 | -0.72 | -0.81 |
| MT-CO2 | -0.72 | -0.82 |
| AF347015.33 | -0.71 | -0.81 |
| AF347015.27 | -0.71 | -0.81 |
| AF347015.8 | -0.69 | -0.82 |
| MT-CYB | -0.69 | -0.80 |
| AF347015.21 | -0.67 | -0.84 |
| C5orf53 | -0.66 | -0.70 |
| AF347015.15 | -0.66 | -0.78 |
| S100B | -0.66 | -0.75 |
Section III. Gene Ontology annotation
| Molecular function | GO term | Evidence | Neuro keywords | PubMed ID |
|---|---|---|---|---|
| GO:0005488 | binding | IEA | - |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| PARENT MTOR SIGNALING UP | 567 | 375 | All SZGR 2.0 genes in this pathway |
| GOZGIT ESR1 TARGETS DN | 781 | 465 | All SZGR 2.0 genes in this pathway |
| SCHLOSSER SERUM RESPONSE UP | 134 | 93 | All SZGR 2.0 genes in this pathway |
| DAUER STAT3 TARGETS DN | 50 | 34 | All SZGR 2.0 genes in this pathway |
| NUYTTEN NIPP1 TARGETS UP | 769 | 437 | All SZGR 2.0 genes in this pathway |
| NUYTTEN EZH2 TARGETS UP | 1037 | 673 | All SZGR 2.0 genes in this pathway |
| PENG RAPAMYCIN RESPONSE UP | 203 | 130 | All SZGR 2.0 genes in this pathway |
| LEIN NEURON MARKERS | 69 | 45 | All SZGR 2.0 genes in this pathway |
| CHANG CORE SERUM RESPONSE DN | 209 | 137 | All SZGR 2.0 genes in this pathway |
| CAIRO HEPATOBLASTOMA CLASSES DN | 210 | 141 | All SZGR 2.0 genes in this pathway |
| ZHAN MULTIPLE MYELOMA MF DN | 41 | 28 | All SZGR 2.0 genes in this pathway |