Gene Page: APEX1

Summary ?
GeneID328
SymbolAPEX1
SynonymsAPE|APE1|APEN|APEX|APX|HAP1|REF1
Descriptionapurinic/apyrimidinic endodeoxyribonuclease 1
ReferenceMIM:107748|HGNC:HGNC:587|Ensembl:ENSG00000100823|HPRD:00136|Vega:OTTHUMG00000029544
Gene typeprotein-coding
Map location14q11.2
Pascal p-value0.716
Sherlock p-value0.724
Fetal beta1.364
DMG1 (# studies)

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
DMG:Nishioka_2013Genome-wide DNA methylation analysisThe authors investigated the methylation profiles of DNA in peripheral blood cells from 18 patients with first-episode schizophrenia (FESZ) and from 15 normal controls. 1
GSMA_IGenome scan meta-analysisPsr: 0.047 
NetworkShortest path distance of core genes in the Human protein-protein interaction networkContribution to shortest path in PPI network: 0.0385 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg224383241420922915APEX1-0.0230.34DMG:Nishioka_2013


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
HOOK30.920.92
UTP14C0.910.92
TMF10.910.93
ZNF7910.890.91
CLPX0.890.90
RABGAP10.890.91
ATRX0.890.91
C9orf1020.890.91
SEC630.890.90
UGCGL10.880.91
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
AF347015.31-0.68-0.73
FXYD1-0.67-0.72
HIGD1B-0.67-0.73
MT-CO2-0.67-0.72
ENHO-0.66-0.77
AF347015.21-0.66-0.72
IFI27-0.66-0.72
METRN-0.64-0.71
CST3-0.63-0.70
AF347015.27-0.63-0.67

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0000287magnesium ion bindingIEA-
GO:0003677DNA bindingIDA11286553 
GO:0003713transcription coactivator activityIDA9119221 
GO:0003714transcription corepressor activityTAS7961715 
GO:0003906DNA-(apurinic or apyrimidinic site) lyase activityTAS9119221 
GO:0005515protein bindingIPI12524539 |15518571 
GO:0004844uracil DNA N-glycosylase activityTAS10805771 
GO:0004520endodeoxyribonuclease activityTAS1722334 
GO:0004523ribonuclease H activityTAS11286553 
GO:0004528phosphodiesterase I activityTAS9119221 
GO:0016829lyase activityIEA-
GO:00084083'-5' exonuclease activityTAS11286553 
GO:0016491oxidoreductase activityIDA9119221 
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0006366transcription from RNA polymerase II promoterTAS1380454 
GO:0006284base-excision repairTAS11286553 
GO:0051101regulation of DNA bindingIDA9119221 
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005813centrosomeIDA18029348 
GO:0005840ribosomeTAS12524539 
GO:0005622intracellularIEA-
GO:0005634nucleusIDA9119221 
GO:0005654nucleoplasmEXP9207062 |10559261 |11250913 
GO:0005737cytoplasmIEA-
GO:0005783endoplasmic reticulumTAS12524539 
GO:0048471perinuclear region of cytoplasmIDA12524539 

Section IV. Protein-protein interaction annotation

InteractorsAliases BOfficial full name BExperimentalSourcePubMed ID
ANP32AC15orf1 | I1PP2A | LANP | MAPM | MGC119787 | MGC150373 | PHAP1 | PHAPI | PP32acidic (leucine-rich) nuclear phosphoprotein 32 family, member AAffinity Capture-WesternBioGRID12524539 
CDKN1ACAP20 | CDKN1 | CIP1 | MDA-6 | P21 | SDI1 | WAF1 | p21CIP1cyclin-dependent kinase inhibitor 1A (p21, Cip1)Ref1 interacts weakly with p21 promoter.BIND15674341 
DCTN1DAP-150 | DP-150 | HMN7B | P135dynactin 1 (p150, glued homolog, Drosophila)-HPRD9361024 
FEN1FEN-1 | MF1 | RAD2flap structure-specific endonuclease 1-HPRD,BioGRID11601988 
HIF1AHIF-1alpha | HIF1 | HIF1-ALPHA | MOP1 | PASD8hypoxia-inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)-HPRD,BioGRID10594042 
HMGB2HMG2high-mobility group box 2-HPRD12524539 
HNRNPLFLJ35509 | HNRPL | P/OKcl.14 | hnRNP-Lheterogeneous nuclear ribonucleoprotein L-HPRD,BioGRID11809897 
HSPA1AFLJ54303 | FLJ54370 | FLJ54392 | FLJ54408 | FLJ75127 | HSP70-1 | HSP70-1A | HSP70I | HSP72 | HSPA1 | HSPA1Bheat shock 70kDa protein 1A-HPRD11133992 
MUTYHMGC4416 | MYHmutY homolog (E. coli)hMYH is associated in vivo with apurinic/apyrimidinic endonuclease (APE1)BIND11092888 
MUTYHMGC4416 | MYHmutY homolog (E. coli)-HPRD,BioGRID11092888 
NME1AWD | GAAD | NB | NBS | NDPK-A | NDPKA | NM23 | NM23-H1non-metastatic cells 1, protein (NM23A) expressed in-HPRD12524539 
PCNAMGC8367proliferating cell nuclear antigen-HPRD,BioGRID11601988 
SET2PP2A | I2PP2A | IGAAD | IPP2A2 | PHAPII | TAF-I | TAF-IBETASET nuclear oncogene-HPRD12628186 
SET2PP2A | I2PP2A | IGAAD | IPP2A2 | PHAPII | TAF-I | TAF-IBETASET nuclear oncogeneAffinity Capture-WesternBioGRID12524539 
TP53FLJ92943 | LFS1 | TRP53 | p53tumor protein p53p53 interacts with Ref-1.BIND15824742 
TP53FLJ92943 | LFS1 | TRP53 | p53tumor protein p53-HPRD,BioGRID9119221 
TXNDKFZp686B1993 | MGC61975 | TRX | TRX1thioredoxin-HPRD10585464|11118054 
UBE2IC358B7.1 | P18 | UBC9ubiquitin-conjugating enzyme E2I (UBC9 homolog, yeast)-HPRD,BioGRID12110916 
XRCC1RCCX-ray repair complementing defective repair in Chinese hamster cells 1-HPRD,BioGRID11707423 
XRCC5FLJ39089 | KARP-1 | KARP1 | KU80 | KUB2 | Ku86 | NFIVX-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)Reconstituted ComplexBioGRID8621488 
XRCC6CTC75 | CTCBF | G22P1 | KU70 | ML8 | TLAAX-ray repair complementing defective repair in Chinese hamster cells 6-HPRD8621488 


Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG BASE EXCISION REPAIR 3522All SZGR 2.0 genes in this pathway
BIOCARTA SET PATHWAY 116All SZGR 2.0 genes in this pathway
PID HIF2PATHWAY 3429All SZGR 2.0 genes in this pathway
REACTOME BASE EXCISION REPAIR 1913All SZGR 2.0 genes in this pathway
REACTOME RESOLUTION OF AP SITES VIA THE MULTIPLE NUCLEOTIDE PATCH REPLACEMENT PATHWAY 1711All SZGR 2.0 genes in this pathway
REACTOME BASE FREE SUGAR PHOSPHATE REMOVAL VIA THE SINGLE NUCLEOTIDE REPLACEMENT PATHWAY 105All SZGR 2.0 genes in this pathway
REACTOME DNA REPAIR 11259All SZGR 2.0 genes in this pathway
REACTOME RESOLUTION OF AP SITES VIA THE SINGLE NUCLEOTIDE REPLACEMENT PATHWAY 127All SZGR 2.0 genes in this pathway
RHEIN ALL GLUCOCORTICOID THERAPY DN 362238All SZGR 2.0 genes in this pathway
HAHTOLA MYCOSIS FUNGOIDES SKIN UP 177113All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN DN 17811082All SZGR 2.0 genes in this pathway
GRAESSMANN RESPONSE TO MC AND DOXORUBICIN DN 770415All SZGR 2.0 genes in this pathway
WAKASUGI HAVE ZNF143 BINDING SITES 5833All 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
LOPEZ MBD TARGETS 957597All SZGR 2.0 genes in this pathway
BENPORATH SOX2 TARGETS 734436All SZGR 2.0 genes in this pathway
BENPORATH MYC TARGETS WITH EBOX 230156All SZGR 2.0 genes in this pathway
KAUFFMANN DNA REPAIR GENES 230137All SZGR 2.0 genes in this pathway
MENSSEN MYC TARGETS 5335All SZGR 2.0 genes in this pathway
SMITH TERT TARGETS DN 8769All SZGR 2.0 genes in this pathway
SANA RESPONSE TO IFNG DN 8556All SZGR 2.0 genes in this pathway
FERRANDO LYL1 NEIGHBORS 1512All SZGR 2.0 genes in this pathway
SANSOM APC TARGETS UP 12684All SZGR 2.0 genes in this pathway
LEI MYB TARGETS 318215All SZGR 2.0 genes in this pathway
BROWN MYELOID CELL DEVELOPMENT DN 12986All SZGR 2.0 genes in this pathway
NEMETH INFLAMMATORY RESPONSE LPS DN 3225All SZGR 2.0 genes in this pathway
NGUYEN NOTCH1 TARGETS DN 8667All SZGR 2.0 genes in this pathway
JAZAERI BREAST CANCER BRCA1 VS BRCA2 DN 4331All SZGR 2.0 genes in this pathway
HEDENFALK BREAST CANCER HEREDITARY VS SPORADIC 5032All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN 1237837All SZGR 2.0 genes in this pathway
HARRIS HYPOXIA 8164All SZGR 2.0 genes in this pathway
PAL PRMT5 TARGETS UP 203135All SZGR 2.0 genes in this pathway
HU GENOTOXIN ACTION DIRECT VS INDIRECT 24HR 5538All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS INTERMEDIATE PROGENITOR 14984All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 UP 428266All SZGR 2.0 genes in this pathway
WELCSH BRCA1 TARGETS DN 14192All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 12HR DN 10164All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 1 528324All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 4 307185All SZGR 2.0 genes in this pathway
ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE UP 863514All SZGR 2.0 genes in this pathway
GRADE COLON CANCER UP 871505All SZGR 2.0 genes in this pathway
ALONSO METASTASIS UP 198128All SZGR 2.0 genes in this pathway
MUELLER PLURINET 299189All SZGR 2.0 genes in this pathway
SWEET LUNG CANCER KRAS UP 491316All SZGR 2.0 genes in this pathway
HSIAO HOUSEKEEPING GENES 389245All SZGR 2.0 genes in this pathway
IRITANI MAD1 TARGETS DN 4730All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA CLASSES UP 605377All SZGR 2.0 genes in this pathway
DANG MYC TARGETS UP 143100All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC 1103714All SZGR 2.0 genes in this pathway
WONG EMBRYONIC STEM CELL CORE 335193All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 14 14386All SZGR 2.0 genes in this pathway
KIM BIPOLAR DISORDER OLIGODENDROCYTE DENSITY CORR UP 682440All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN 19721213All SZGR 2.0 genes in this pathway
DELPUECH FOXO3 TARGETS DN 4127All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS DN 882538All SZGR 2.0 genes in this pathway
FEVR CTNNB1 TARGETS DN 553343All SZGR 2.0 genes in this pathway