Gene Page:URB2
Summary?
| GeneID | 9816 |
| Symbol | URB2 |
| Synonyms | KIAA0133|NET10|NPA2 |
| Description | URB2 ribosome biogenesis 2 homolog (S. cerevisiae) |
| Reference | HGNC:HGNC:28967|Ensembl:ENSG00000135763|HPRD:17178|Vega:OTTHUMG00000039464 |
| Gene type | protein-coding |
| Map location | 1q42.13 |
| TADA p-value | 0.004 |
| Fetal beta | 0.62 |
| DMG | 1 (# studies) |
| eGene | 元 |
| Support | CompositeSet Ascano FMRP targets |
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. | 2 |
| 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). | 2 |
| DNM:Xu_2012 | Whole Exome Sequencing analysis | 新创的突变4基因被确定by exome sequencing of 795 samples in this study |
Section I. Genetics and epigenetics annotation
DNM table
DNM table| Gene | Chromosome | Position | Ref | Alt | Transcript | AA change | Mutation type | Sift | CG46 | Trait | Study |
|---|---|---|---|---|---|---|---|---|---|---|---|
| URB2 | chr1 | 229783350 | G | T | NM_014777 | p.1334E>* | nonsense | Schizophrenia | DNM:Xu_2012 |
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg22873177 | 1 | 229761584 | URB2;TAF5L | 1.78E-5 | -0.246 | 0.016 | DMG:Wockner_2014 |
| cg04122790 | 1 | 229762148 | URB2 | 3.38E-11 | -0.026 | 3.6E-7 | DMG:Jaffe_2016 |
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 |
| NONO | 0.97 | 0.89 |
| RBMX | 0.96 | 0.87 |
| GNAI3 | 0.95 | 0.91 |
| EIF4B | 0.95 | 0.82 |
| XRN2 | 0.95 | 0.89 |
| KDM1 | 0.94 | 0.87 |
| FUBP1 | 0.94 | 0.88 |
| INTS7 | 0.94 | 0.83 |
| NUP88 | 0.93 | 0.83 |
| ANP32A | 0.93 | 0.84 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| C5orf53 | -0.66 | -0.74 |
| TNFSF12 | -0.65 | -0.65 |
| FBXO2 | -0.65 | -0.69 |
| HLA-F | -0.65 | -0.75 |
| LHPP | -0.65 | -0.59 |
| PTH1R | -0.63 | -0.68 |
| AIFM3 | -0.63 | -0.68 |
| SLC16A11 | -0.63 | -0.65 |
| ASPHD1 | -0.62 | -0.62 |
| LDHD | -0.62 | -0.62 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| GINESTIER BREAST CANCER ZNF217 AMPLIFIED DN | 335 | 193 | All SZGR 2.0 genes in this pathway |
| ELVIDGE HYPOXIA DN | 146 | 94 | All SZGR 2.0 genes in this pathway |
| ELVIDGE HYPOXIA BY DMOG DN | 59 | 40 | All SZGR 2.0 genes in this pathway |
| ELVIDGE HIF1A TARGETS UP | 67 | 40 | All SZGR 2.0 genes in this pathway |
| DODD NASOPHARYNGEAL CARCINOMA DN | 1375 | 806 | 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 |
| WEI MYCN TARGETS WITH E BOX | 795 | 478 | All SZGR 2.0 genes in this pathway |
| LIAO METASTASIS | 539 | 324 | All SZGR 2.0 genes in this pathway |
| MANALO HYPOXIA DN | 289 | 166 | All SZGR 2.0 genes in this pathway |
| MONNIER POSTRADIATION TUMOR ESCAPE UP | 393 | 244 | All SZGR 2.0 genes in this pathway |
| HOSHIDA LIVER CANCER LATE RECURRENCE DN | 69 | 48 | All SZGR 2.0 genes in this pathway |
| MIKKELSEN MCV6 LCP WITH H3K4ME3 | 162 | 80 | All SZGR 2.0 genes in this pathway |
| WANG RESPONSE TO GSK3 INHIBITOR SB216763 DN | 374 | 217 | All SZGR 2.0 genes in this pathway |
| LEE BMP2 TARGETS DN | 882 | 538 | All SZGR 2.0 genes in this pathway |
| VANOEVELEN MYOGENESIS SIN3A TARGETS | 220 | 133 | All SZGR 2.0 genes in this pathway |
| ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY | 1725 | 838 | All SZGR 2.0 genes in this pathway |