Gene Page: H2AFX

Summary ?
GeneID3014
SymbolH2AFX
SynonymsH2A.X|H2A/X|H2AX
DescriptionH2A histone family member X
ReferenceMIM:601772|HGNC:HGNC:4739|Ensembl:ENSG00000188486|HPRD:03465|Vega:OTTHUMG00000166196
Gene typeprotein-coding
Map location11q23.3
Pascal p-value0.035
Sherlock p-value0.417
Fetal beta0.647
DMG1 (# studies)
eGeneMyers' cis & trans

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
GSMA_IGenome scan meta-analysisPsr: 0.006 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg0615943511118966351H2AFX9.9E-6-0.4610.013DMG:Wockner_2014

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs4706060chr679232160H2AFX30140.2trans

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.

No co-expressed genes in brain regions


Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0003684damaged DNA bindingIEA-
GO:0005515protein bindingIPI17498979 
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0000724double-strand break repair via homologous recombinationIEA-
GO:0006334nucleosome assemblyNAS2587254 
GO:0006310DNA recombinationIEA-
GO:0007283spermatogenesisIEA-
GO:0006281DNA repairIEA-
GO:0007049cell cycleIEA-
GO:0007126meiosisIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0000786nucleosomeNAS-
GO:0005634nucleusIDA11331621 |15604234 
GO:0005654nucleoplasmEXP10959836 |12419185 |12556884 
GO:0005657replication forkIEA-
GO:0005694chromosomeIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG SYSTEMIC LUPUS ERYTHEMATOSUS 140100All SZGR 2.0 genes in this pathway
PID FANCONI PATHWAY 4728All SZGR 2.0 genes in this pathway
PID ATM PATHWAY 3425All SZGR 2.0 genes in this pathway
REACTOME MEIOSIS 11681All SZGR 2.0 genes in this pathway
REACTOME CELL CYCLE 421253All SZGR 2.0 genes in this pathway
REACTOME RNA POL I TRANSCRIPTION 8964All SZGR 2.0 genes in this pathway
REACTOME HOMOLOGOUS RECOMBINATION REPAIR OF REPLICATION INDEPENDENT DOUBLE STRAND BREAKS 1711All SZGR 2.0 genes in this pathway
REACTOME TRANSCRIPTION 210127All SZGR 2.0 genes in this pathway
REACTOME DOUBLE STRAND BREAK REPAIR 2414All SZGR 2.0 genes in this pathway
REACTOME RNA POL I RNA POL III AND MITOCHONDRIAL TRANSCRIPTION 12280All SZGR 2.0 genes in this pathway
REACTOME DNA REPAIR 11259All SZGR 2.0 genes in this pathway
REACTOME CHROMOSOME MAINTENANCE 12280All SZGR 2.0 genes in this pathway
REACTOME DEPOSITION OF NEW CENPA CONTAINING NUCLEOSOMES AT THE CENTROMERE 6443All SZGR 2.0 genes in this pathway
REACTOME RNA POL I PROMOTER OPENING 6249All SZGR 2.0 genes in this pathway
REACTOME MEIOTIC RECOMBINATION 8662All SZGR 2.0 genes in this pathway
REACTOME MEIOTIC SYNAPSIS 7357All SZGR 2.0 genes in this pathway
REACTOME AMYLOIDS 8363All SZGR 2.0 genes in this pathway
REACTOME PACKAGING OF TELOMERE ENDS 4840All SZGR 2.0 genes in this pathway
REACTOME TELOMERE MAINTENANCE 7557All SZGR 2.0 genes in this pathway
ONKEN UVEAL MELANOMA UP 783507All SZGR 2.0 genes in this pathway
GAZDA DIAMOND BLACKFAN ANEMIA ERYTHROID DN 493298All SZGR 2.0 genes in this pathway
FULCHER INFLAMMATORY RESPONSE LECTIN VS LPS UP 579346All SZGR 2.0 genes in this pathway
DEURIG T CELL PROLYMPHOCYTIC LEUKEMIA UP 368234All SZGR 2.0 genes in this pathway
HORIUCHI WTAP TARGETS DN 310188All SZGR 2.0 genes in this pathway
BASAKI YBX1 TARGETS UP 290177All SZGR 2.0 genes in this pathway
WANG LMO4 TARGETS UP 372227All SZGR 2.0 genes in this pathway
SENESE HDAC3 TARGETS DN 536332All SZGR 2.0 genes in this pathway
GRAHAM CML QUIESCENT VS NORMAL QUIESCENT UP 8745All SZGR 2.0 genes in this pathway
GRAHAM CML DIVIDING VS NORMAL QUIESCENT UP 181101All SZGR 2.0 genes in this pathway
ENK UV RESPONSE KERATINOCYTE UP 530342All SZGR 2.0 genes in this pathway
DELYS THYROID CANCER UP 443294All SZGR 2.0 genes in this pathway
CHIARADONNA NEOPLASTIC TRANSFORMATION KRAS UP 12672All SZGR 2.0 genes in this pathway
CHIARADONNA NEOPLASTIC TRANSFORMATION CDC25 UP 12073All SZGR 2.0 genes in this pathway
MARKEY RB1 ACUTE LOF DN 228137All SZGR 2.0 genes in this pathway
KONG E2F1 TARGETS 106All SZGR 2.0 genes in this pathway
KONG E2F3 TARGETS 9758All SZGR 2.0 genes in this pathway
LASTOWSKA NEUROBLASTOMA COPY NUMBER DN 800473All SZGR 2.0 genes in this pathway
EBAUER TARGETS OF PAX3 FOXO1 FUSION UP 207128All SZGR 2.0 genes in this pathway
RASHI RESPONSE TO IONIZING RADIATION 4 6134All SZGR 2.0 genes in this pathway
ROSTY CERVICAL CANCER PROLIFERATION CLUSTER 14073All SZGR 2.0 genes in this pathway
PATIL LIVER CANCER 747453All SZGR 2.0 genes in this pathway
OXFORD RALA OR RALB TARGETS UP 4823All SZGR 2.0 genes in this pathway
MOHANKUMAR TLX1 TARGETS UP 414287All SZGR 2.0 genes in this pathway
SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN UP 479299All SZGR 2.0 genes in this pathway
PUJANA BREAST CANCER LIT INT NETWORK 10173All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK 16521023All SZGR 2.0 genes in this pathway
PUJANA BRCA2 PCC NETWORK 423265All SZGR 2.0 genes in this pathway
GROSS HYPOXIA VIA ELK3 UP 209139All SZGR 2.0 genes in this pathway
NUYTTEN NIPP1 TARGETS DN 848527All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS DN 1024594All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS DN 637377All SZGR 2.0 genes in this pathway
BENPORATH NANOG TARGETS 988594All SZGR 2.0 genes in this pathway
BENPORATH SOX2 TARGETS 734436All SZGR 2.0 genes in this pathway
BENPORATH EED TARGETS 1062725All SZGR 2.0 genes in this pathway
BENPORATH MYC MAX TARGETS 775494All SZGR 2.0 genes in this pathway
BENPORATH CYCLING GENES 648385All SZGR 2.0 genes in this pathway
AMIT EGF RESPONSE 480 HELA 164118All SZGR 2.0 genes in this pathway
SHIN B CELL LYMPHOMA CLUSTER 8 3628All SZGR 2.0 genes in this pathway
MORI PRE BI LYMPHOCYTE UP 8054All SZGR 2.0 genes in this pathway
MORI LARGE PRE BII LYMPHOCYTE UP 8649All SZGR 2.0 genes in this pathway
MORI IMMATURE B LYMPHOCYTE DN 9055All SZGR 2.0 genes in this pathway
COLLIS PRKDC SUBSTRATES 2015All SZGR 2.0 genes in this pathway
KAUFFMANN DNA REPAIR GENES 230137All SZGR 2.0 genes in this pathway
MANALO HYPOXIA DN 289166All SZGR 2.0 genes in this pathway
LE EGR2 TARGETS UP 10875All SZGR 2.0 genes in this pathway
REN BOUND BY E2F 6140All SZGR 2.0 genes in this pathway
PENG RAPAMYCIN RESPONSE UP 203130All SZGR 2.0 genes in this pathway
ZHAN V2 LATE DIFFERENTIATION GENES 4534All SZGR 2.0 genes in this pathway
GREENBAUM E2A TARGETS UP 3318All SZGR 2.0 genes in this pathway
LY AGING PREMATURE DN 3017All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 20HR UP 240152All SZGR 2.0 genes in this pathway
HU GENOTOXIC DAMAGE 24HR 3522All SZGR 2.0 genes in this pathway
PAL PRMT5 TARGETS UP 203135All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 8HR UP 10573All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP 16911088All SZGR 2.0 genes in this pathway
KIM GASTRIC CANCER CHEMOSENSITIVITY 10364All SZGR 2.0 genes in this pathway
RHODES UNDIFFERENTIATED CANCER 6944All SZGR 2.0 genes in this pathway
DAZARD RESPONSE TO UV NHEK UP 244151All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS PEAK AT 24HR 4330All SZGR 2.0 genes in this pathway
MODY HIPPOCAMPUS PRENATAL 4233All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 4 4832All SZGR 2.0 genes in this pathway
SONG TARGETS OF IE86 CMV PROTEIN 6042All SZGR 2.0 genes in this pathway
LEE CALORIE RESTRICTION NEOCORTEX DN 8858All SZGR 2.0 genes in this pathway
LY AGING OLD DN 5635All SZGR 2.0 genes in this pathway
WANG CISPLATIN RESPONSE AND XPC UP 202115All SZGR 2.0 genes in this pathway
BANDRES RESPONSE TO CARMUSTIN MGMT 48HR DN 161105All SZGR 2.0 genes in this pathway
LY AGING MIDDLE DN 1610All SZGR 2.0 genes in this pathway
HU GENOTOXIC DAMAGE 4HR 3528All SZGR 2.0 genes in this pathway
SESTO RESPONSE TO UV C3 2015All SZGR 2.0 genes in this pathway
MARSON BOUND BY E2F4 UNSTIMULATED 728415All SZGR 2.0 genes in this pathway
AMUNDSON GAMMA RADIATION RESPONSE 4025All SZGR 2.0 genes in this pathway
SARRIO EPITHELIAL MESENCHYMAL TRANSITION UP 180114All SZGR 2.0 genes in this pathway
FUJII YBX1 TARGETS DN 202132All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER UP 973570All SZGR 2.0 genes in this pathway
ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE UP 863514All SZGR 2.0 genes in this pathway
MATZUK SPERMATOCYTE 7255All SZGR 2.0 genes in this pathway
WHITEFORD PEDIATRIC CANCER MARKERS 11663All SZGR 2.0 genes in this pathway
CHEN HOXA5 TARGETS 9HR DN 4117All SZGR 2.0 genes in this pathway
FRASOR RESPONSE TO SERM OR FULVESTRANT DN 5029All SZGR 2.0 genes in this pathway
GOLDRATH ANTIGEN RESPONSE 346192All SZGR 2.0 genes in this pathway
RUIZ TNC TARGETS DN 14279All SZGR 2.0 genes in this pathway
CHANG CYCLING GENES 14883All SZGR 2.0 genes in this pathway
SWEET LUNG CANCER KRAS DN 435289All SZGR 2.0 genes in this pathway
HOFFMANN LARGE TO SMALL PRE BII LYMPHOCYTE UP 163102All SZGR 2.0 genes in this pathway
SHEDDEN LUNG CANCER POOR SURVIVAL A6 456285All SZGR 2.0 genes in this pathway
CROONQUIST NRAS SIGNALING DN 7247All SZGR 2.0 genes in this pathway
CROONQUIST NRAS VS STROMAL STIMULATION DN 9965All SZGR 2.0 genes in this pathway
KOBAYASHI EGFR SIGNALING 24HR DN 251151All SZGR 2.0 genes in this pathway
CHIARETTI T ALL RELAPSE PROGNOSIS 1915All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC 1103714All SZGR 2.0 genes in this pathway
DAZARD UV RESPONSE CLUSTER G5 128All SZGR 2.0 genes in this pathway
WHITFIELD CELL CYCLE G2 182102All SZGR 2.0 genes in this pathway
MARTENS TRETINOIN RESPONSE DN 841431All SZGR 2.0 genes in this pathway
WANG RESPONSE TO GSK3 INHIBITOR SB216763 DN 374217All SZGR 2.0 genes in this pathway
DUTERTRE ESTRADIOL RESPONSE 24HR UP 324193All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE LATE 1137655All SZGR 2.0 genes in this pathway
LINSLEY MIR16 TARGETS 206127All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION UP 570339All SZGR 2.0 genes in this pathway
PEDERSEN METASTASIS BY ERBB2 ISOFORM 7 403240All SZGR 2.0 genes in this pathway
WAKABAYASHI ADIPOGENESIS PPARG RXRA BOUND 8D 882506All SZGR 2.0 genes in this pathway
ZHOU CELL CYCLE GENES IN IR RESPONSE 6HR 8549All SZGR 2.0 genes in this pathway
ZHOU CELL CYCLE GENES IN IR RESPONSE 24HR 12873All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-1389409461Ahsa-miR-138brainAGCUGGUGUUGUGAAUC
miR-1459929991A,m8hsa-miR-145GUCCAGUUUUCCCAGGAAUCCCUU
miR-22100410101Ahsa-miR-22brainAAGCUGCCAGUUGAAGAACUGU
miR-248894m8hsa-miR-24SZUGGCUCAGUUCAGCAGGAACAG
hsa-miR-24SZUGGCUCAGUUCAGCAGGAACAG
miR-3286066m8hsa-miR-328brainCUGGCCCUCUCUGCCCUUCCGU