Gene Page: POP4
Summary ?
| GeneID | 10775 |
| Symbol | POP4 |
| Synonyms | RPP29 |
| Description | POP4 homolog, ribonuclease P/MRP subunit |
| Reference | MIM:606114|HGNC:HGNC:30081|Ensembl:ENSG00000105171|HPRD:09358|Vega:OTTHUMG00000182020 |
| Gene type | protein-coding |
| Map location | 19q12 |
| Pascal p-value | 0.861 |
| Sherlock p-value | 0.188 |
| Fetal beta | -0.587 |
| DMG | 1 (# studies) |
| eGene | Myers' cis & trans |
| Support | G2Cdb.humanPSD G2Cdb.humanPSP |
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 |
Section I. Genetics and epigenetics annotation
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg22560837 | 19 | 30097072 | POP4 | 1.076E-4 | 0.824 | 0.028 | DMG:Wockner_2014 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs2948491 | chrX | 40180688 | POP4 | 10775 | 0.19 | 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 |
| UBE2N | 0.89 | 0.87 |
| RAB11A | 0.89 | 0.86 |
| YWHAE | 0.88 | 0.88 |
| C11orf58 | 0.88 | 0.86 |
| C16orf94 | 0.88 | 0.85 |
| PTGES3 | 0.88 | 0.87 |
| C10orf84 | 0.87 | 0.84 |
| PSMD10 | 0.87 | 0.87 |
| UBA3 | 0.87 | 0.86 |
| SCCPDH | 0.87 | 0.85 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| MT-CO2 | -0.68 | -0.64 |
| AF347015.2 | -0.67 | -0.66 |
| AF347015.33 | -0.66 | -0.63 |
| MT-CYB | -0.66 | -0.63 |
| AF347015.26 | -0.65 | -0.63 |
| AF347015.8 | -0.65 | -0.62 |
| AF347015.9 | -0.63 | -0.65 |
| AF347015.15 | -0.63 | -0.62 |
| FXYD1 | -0.63 | -0.64 |
| AF347015.31 | -0.63 | -0.61 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| LINDGREN BLADDER CANCER CLUSTER 3 UP | 329 | 196 | All SZGR 2.0 genes in this pathway |
| PUJANA BRCA1 PCC NETWORK | 1652 | 1023 | All SZGR 2.0 genes in this pathway |
| PUJANA ATM PCC NETWORK | 1442 | 892 | All SZGR 2.0 genes in this pathway |
| PUJANA CHEK2 PCC NETWORK | 779 | 480 | All SZGR 2.0 genes in this pathway |
| NUYTTEN EZH2 TARGETS DN | 1024 | 594 | All SZGR 2.0 genes in this pathway |
| WEI MYCN TARGETS WITH E BOX | 795 | 478 | All SZGR 2.0 genes in this pathway |
| RICKMAN TUMOR DIFFERENTIATED MODERATELY VS POORLY UP | 121 | 71 | All SZGR 2.0 genes in this pathway |
| KOYAMA SEMA3B TARGETS UP | 292 | 168 | All SZGR 2.0 genes in this pathway |
| SHEPARD CRUSH AND BURN MUTANT UP | 197 | 110 | All SZGR 2.0 genes in this pathway |
| BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS | 882 | 572 | All SZGR 2.0 genes in this pathway |
| FAELT B CLL WITH VH3 21 DN | 49 | 29 | All SZGR 2.0 genes in this pathway |
| NOUZOVA TRETINOIN AND H4 ACETYLATION | 143 | 85 | All SZGR 2.0 genes in this pathway |
| IVANOVA HEMATOPOIESIS EARLY PROGENITOR | 532 | 309 | All SZGR 2.0 genes in this pathway |
| VANDESLUIS NORMAL EMBRYOS DN | 25 | 13 | All SZGR 2.0 genes in this pathway |
| KRIEG KDM3A TARGETS NOT HYPOXIA | 208 | 107 | All SZGR 2.0 genes in this pathway |