Gene Page:USP39

Summary?
GeneID 10713
Symbol USP39
Synonyms 65K|CGI-21|HSPC332|SAD1|SNRNP65
Description ubiquitin specific peptidase 39
Reference MIM:611594|HGNC:HGNC:20071|Ensembl:ENSG00000168883|HPRD: 07165|Vega:OTTHUMG00000153090
Gene type protein-coding
Map location 2p11.2
Pascal p-value 0.095
Sherlock p-value 0.214
Fetal beta 0.87
DMG 1 (# studies)

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
GSMA_I Genome scan meta-analysis Psr: 0.0004

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

Probe Chromosome Position Nearest gene P (dis) Beta (dis) FDR (dis) Study
ch.2.1892000F 2 85858578 USP39 2.373E-4 -0.168 0.037 DMG:Wockner_2014


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
Gene Pearson's Correlation Spearman's Correlation
SASH3 0.58 0.48
CD68 0.55 0.47
HCK 0.55 0.46
SYK 0.53 0.46
FOLR2 0.52 0.41
NCKAP1L 0.52 0.48
ITGB2 0.51 0.49
CYTH4 0.49 0.44
SIGLEC7 0.48 0.34
CD37 0.48 0.43
Top 10 negatively co-expressed genes
Gene Pearson's Correlation Spearman's Correlation
AF347015.18 -0.19 -0.17
MT-CO2 -0.18 -0.15
AC010300.1 -0.18 -0.15
NOSTRIN -0.18 -0.12
EDN1 -0.17 -0.06
CXCL2 -0.17 -0.13
ANP32C -0.17 -0.12
F2RL3 -0.17 -0.08
IL32 -0.16 -0.13
AF347015.26 -0.16 -0.13

Section III. Gene Ontology annotation

Molecular function 去term Evidence Neuro keywords PubMed ID
去:0005515 protein binding 新闻学会 17353931
去:0004221 泛素thiolesterase活动 IEA -
去:0008270 zinc ion binding IEA -
去:0046872 metal ion binding IEA -
Biological process 去term Evidence Neuro keywords PubMed ID
去:0000245 spliceosome assembly TAS 10022888
去:0006397 mRNA processing TAS 10022888
去:0008380 RNA splicing TAS 10022888
去:0006511 ubiquitin-dependent protein catabolic process IEA -
Cellular component 去term Evidence Neuro keywords PubMed ID
去:0005622 intracellular IEA -
去:0005634 nucleus IEA -

Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
KEGG SPLICEOSOME 128 72 All SZGR 2.0 genes in this pathway
NAKAMURA CANCER MICROENVIRONMENT DN 46 29 All SZGR 2.0 genes in this pathway
KINSEY TARGETS OF EWSR1 FLII FUSION UP 1278 748 All SZGR 2.0 genes in this pathway
STARK PREFRONTAL CORTEX 22Q11 DELETION DN 517 309 All SZGR 2.0 genes in this pathway
MANALO HYPOXIA DN 289 166 All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS 882 572 All SZGR 2.0 genes in this pathway
DOUGLAS BMI1 TARGETS UP 566 371 All SZGR 2.0 genes in this pathway
WONG PROTEASOME GENE MODULE 49 35 All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER WITH H3K9ME3 DN 120 71 All SZGR 2.0 genes in this pathway
KUROKAWA LIVER CANCER EARLY RECURRENCE UP 12 9 All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 11 103 68 All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN 1972 1213 All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS DN 882 538 All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA family Target position miRNA ID miRNA seq
UTR start UTR end Match method
miR-299-5p 469 475 1A hsa-miR-299-5p UGGUUUACCGUCCCACAUACAU