Gene Page: URB2

Summary ?
GeneID9816
SymbolURB2
SynonymsKIAA0133|NET10|NPA2
DescriptionURB2 ribosome biogenesis 2 homolog (S. cerevisiae)
ReferenceHGNC:HGNC:28967|Ensembl:ENSG00000135763|HPRD:17178|Vega:OTTHUMG00000039464
Gene typeprotein-coding
Map location1q42.13
TADA p-value0.004
Fetal beta0.62
DMG1 (# studies)
eGeneMeta
SupportCompositeSet
Ascano FMRP targets

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Jaffe_2016Genome-wide DNA methylation analysisThis 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_2014Genome-wide DNA methylation analysisThis dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24). 2
DNM:Xu_2012Whole Exome Sequencing analysisDe novo mutations of 4 genes were identified by exome sequencing of 795 samples in this study

Section I. Genetics and epigenetics annotation

@DNM table

GeneChromosomePositionRefAltTranscriptAA changeMutation typeSiftCG46TraitStudy
URB2chr1229783350GTNM_014777p.1334E>*nonsenseSchizophreniaDNM:Xu_2012

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg228731771229761584URB2;TAF5L1.78E-5-0.2460.016DMG:Wockner_2014
cg041227901229762148URB23.38E-11-0.0263.6E-7DMG:Jaffe_2016


Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

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
GenePearson's Correlation Spearman's Correlation
NONO0.970.89
RBMX0.960.87
GNAI30.950.91
EIF4B0.950.82
XRN20.950.89
KDM10.940.87
FUBP10.940.88
INTS70.940.83
NUP880.930.83
ANP32A0.930.84
Top 10 negatively co-expressed genes
GenePearson'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 namePathway size# SZGR 2.0 genes in pathwayInfo
GINESTIER BREAST CANCER ZNF217 AMPLIFIED DN 335193All SZGR 2.0 genes in this pathway
ELVIDGE HYPOXIA DN 14694All SZGR 2.0 genes in this pathway
ELVIDGE HYPOXIA BY DMOG DN 5940All SZGR 2.0 genes in this pathway
ELVIDGE HIF1A TARGETS UP 6740All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA DN 1375806All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK 16521023All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK 1442892All SZGR 2.0 genes in this pathway
PUJANA CHEK2 PCC NETWORK 779480All SZGR 2.0 genes in this pathway
WEI MYCN TARGETS WITH E BOX 795478All SZGR 2.0 genes in this pathway
LIAO METASTASIS 539324All SZGR 2.0 genes in this pathway
MANALO HYPOXIA DN 289166All SZGR 2.0 genes in this pathway
MONNIER POSTRADIATION TUMOR ESCAPE UP 393244All SZGR 2.0 genes in this pathway
HOSHIDA LIVER CANCER LATE RECURRENCE DN 6948All SZGR 2.0 genes in this pathway
MIKKELSEN MCV6 LCP WITH H3K4ME3 16280All SZGR 2.0 genes in this pathway
WANG RESPONSE TO GSK3 INHIBITOR SB216763 DN 374217All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS DN 882538All SZGR 2.0 genes in this pathway
VANOEVELEN MYOGENESIS SIN3A TARGETS 220133All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY 1725838All SZGR 2.0 genes in this pathway