Gene Page: KDM4B

Summary ?
GeneID23030
SymbolKDM4B
SynonymsJMJD2B|TDRD14B
Descriptionlysine demethylase 4B
ReferenceMIM:609765|HGNC:HGNC:29136|Ensembl:ENSG00000127663|HPRD:11056|Vega:OTTHUMG00000180281
Gene typeprotein-coding
Map location19p13.3
Pascal p-value0.025
Sherlock p-value0.667
Fetal beta1.353
DMG1 (# studies)
eGeneMyers' cis & trans
SupportCompositeSet
Darnell FMRP targets
Ascano FMRP targets
Chromatin Remodeling Genes

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
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). 1

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg24450508195141352KDM4B1.855E-40.5230.034DMG:Wockner_2014

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs1368303chr5147672388KDM4B230300trans
rs968370chr84053046KDM4B230300.17trans
rs1902408chr1033873360KDM4B230300.18trans
rs17104720chr1477127308KDM4B230300.08trans
rs16955618chr1529937543KDM4B230300.01trans

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
INTS30.890.91
ZNF8620.860.88
ARHGAP170.850.84
WDR590.850.89
SETD50.840.87
TTLL50.840.86
SLC46A10.840.86
GOLGA10.840.85
ODF20.840.88
COG70.840.85
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
AF347015.31-0.71-0.77
MT-CO2-0.70-0.77
AF347015.27-0.69-0.75
AF347015.21-0.66-0.79
AF347015.8-0.66-0.75
AF347015.33-0.65-0.71
MT-CYB-0.65-0.72
HIGD1B-0.62-0.71
AF347015.2-0.62-0.74
IFI27-0.62-0.68

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0003676nucleic acid bindingIEA-
GO:0005506iron ion bindingIEA-
GO:0005515protein bindingIEA-
GO:0008270zinc ion bindingIEA-
GO:0016702oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygenIEA-
GO:0016491oxidoreductase activityIEA-
GO:0046872metal ion bindingIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0006355regulation of transcription, DNA-dependentIEA-
GO:0006350transcriptionIEA-
GO:0016568chromatin modificationIEA-
GO:0055114oxidation reductionIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005634nucleusIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
PARENT MTOR SIGNALING UP 567375All SZGR 2.0 genes in this pathway
NAKAMURA TUMOR ZONE PERIPHERAL VS CENTRAL DN 634384All SZGR 2.0 genes in this pathway
GAZDA DIAMOND BLACKFAN ANEMIA ERYTHROID DN 493298All SZGR 2.0 genes in this pathway
GARY CD5 TARGETS UP 473314All SZGR 2.0 genes in this pathway
CHARAFE BREAST CANCER LUMINAL VS BASAL UP 380215All SZGR 2.0 genes in this pathway
DOANE RESPONSE TO ANDROGEN UP 184125All SZGR 2.0 genes in this pathway
BASAKI YBX1 TARGETS DN 384230All SZGR 2.0 genes in this pathway
OSWALD HEMATOPOIETIC STEM CELL IN COLLAGEN GEL UP 233161All SZGR 2.0 genes in this pathway
ELVIDGE HYPOXIA UP 171112All SZGR 2.0 genes in this pathway
ELVIDGE HIF1A TARGETS DN 9158All SZGR 2.0 genes in this pathway
ELVIDGE HIF1A AND HIF2A TARGETS DN 10472All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA POORLY DIFFERENTIATED DN 805505All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN DN 17811082All SZGR 2.0 genes in this pathway
PEREZ TP53 TARGETS 1174695All SZGR 2.0 genes in this pathway
FARMER BREAST CANCER APOCRINE VS BASAL 330217All SZGR 2.0 genes in this pathway
FARMER BREAST CANCER BASAL VS LULMINAL 330215All SZGR 2.0 genes in this pathway
SCHLOSSER SERUM RESPONSE UP 13493All SZGR 2.0 genes in this pathway
YANG BREAST CANCER ESR1 UP 3622All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS UP 811508All SZGR 2.0 genes in this pathway
ROSS ACUTE MYELOID LEUKEMIA CBF 8257All SZGR 2.0 genes in this pathway
PENG RAPAMYCIN RESPONSE UP 203130All SZGR 2.0 genes in this pathway
ROSS AML WITH AML1 ETO FUSION 7655All SZGR 2.0 genes in this pathway
MENSE HYPOXIA UP 9871All SZGR 2.0 genes in this pathway
KIM GASTRIC CANCER CHEMOSENSITIVITY 10364All SZGR 2.0 genes in this pathway
MARTINEZ RESPONSE TO TRABECTEDIN DN 271175All SZGR 2.0 genes in this pathway
BILD E2F3 ONCOGENIC SIGNATURE 246153All SZGR 2.0 genes in this pathway
BILD SRC ONCOGENIC SIGNATURE 6238All SZGR 2.0 genes in this pathway
BILD CTNNB1 ONCOGENIC SIGNATURE 8252All SZGR 2.0 genes in this pathway
MASSARWEH TAMOXIFEN RESISTANCE DN 258160All SZGR 2.0 genes in this pathway
OUILLETTE CLL 13Q14 DELETION UP 7440All SZGR 2.0 genes in this pathway
SMID BREAST CANCER RELAPSE IN BRAIN DN 8558All SZGR 2.0 genes in this pathway
SMID BREAST CANCER LUMINAL B UP 172109All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL DN 701446All SZGR 2.0 genes in this pathway
WEST ADRENOCORTICAL TUMOR UP 294199All SZGR 2.0 genes in this pathway
BOHN PRIMARY IMMUNODEFICIENCY SYNDROM DN 4031All SZGR 2.0 genes in this pathway
VANTVEER BREAST CANCER ESR1 UP 16799All SZGR 2.0 genes in this pathway
SHEDDEN LUNG CANCER GOOD SURVIVAL A5 7032All SZGR 2.0 genes in this pathway
VALK AML CLUSTER 13 3020All SZGR 2.0 genes in this pathway
POOLA INVASIVE BREAST CANCER DN 13483All SZGR 2.0 genes in this pathway
YAGI AML WITH T 8 21 TRANSLOCATION 368247All SZGR 2.0 genes in this pathway
QI HYPOXIA 14096All SZGR 2.0 genes in this pathway
FIGUEROA AML METHYLATION CLUSTER 1 DN 4830All SZGR 2.0 genes in this pathway
FIGUEROA AML METHYLATION CLUSTER 3 DN 4224All SZGR 2.0 genes in this pathway
BHAT ESR1 TARGETS NOT VIA AKT1 UP 211131All SZGR 2.0 genes in this pathway
BHAT ESR1 TARGETS VIA AKT1 UP 281183All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP A 898516All SZGR 2.0 genes in this pathway
FOSTER KDM1A TARGETS DN 211119All SZGR 2.0 genes in this pathway
HOLLEMAN VINCRISTINE RESISTANCE B ALL UP 3822All SZGR 2.0 genes in this pathway
HOLLEMAN VINCRISTINE RESISTANCE ALL UP 2716All SZGR 2.0 genes in this pathway