Gene Page: CDKN2A

Summary ?
GeneID1029
SymbolCDKN2A
SynonymsARF|CDK4I|CDKN2|CMM2|INK4|INK4A|MLM|MTS-1|MTS1|P14|P14ARF|P16|P16-INK4A|P16INK4|P16INK4A|P19|P19ARF|TP16
Descriptioncyclin-dependent kinase inhibitor 2A
ReferenceMIM:600160|HGNC:HGNC:1787|Ensembl:ENSG00000147889|HPRD:02542|Vega:OTTHUMG00000019686
Gene typeprotein-coding
Map location9p21
Pascal p-value0.032
Fetal beta-0.468
DMG1 (# studies)
eGeneMyers' cis & trans

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
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
NetworkShortest path distance of core genes in the Human protein-protein interaction networkContribution to shortest path in PPI network: 0.0889 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg00718440921995312CDKN2A-0.0260.35DMG:Nishioka_2013

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs10994209chr1061877705CDKN2A10290.18trans

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:0003677DNA bindingIEA-
GO:0005515protein bindingIPI11278317 |12740913 |15989956 
|17274640 |17909018 
GO:0004861cyclin-dependent protein kinase inhibitor activityIDA8259215 
GO:0051059NF-kappaB bindingIDA10353611 
GO:0019901protein kinase bindingIPI8259215 
GO:0055105ubiquitin-protein ligase inhibitor activityISS-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0000075cell cycle checkpointIMP16243918 
GO:0000082G1/S transition of mitotic cell cycleIDA10208428 
GO:0001953negative regulation of cell-matrix adhesionIMP10205165 
GO:0006309DNA fragmentation during apoptosisIMP12082630 
GO:0006355regulation of transcription, DNA-dependentIEA-
GO:0006350transcriptionIEA-
GO:0006469negative regulation of protein kinase activityIMP15582998 
GO:0006364rRNA processingIEA-
GO:0006917induction of apoptosisIDA10208428 
GO:0006917induction of apoptosisIMP12082630 
GO:0007050cell cycle arrestIMP15582998 |16243918 
GO:0008285negative regulation of cell proliferationIMP16243918 
GO:0008637apoptotic mitochondrial changesIMP12082630 
GO:0010149senescenceIMP14720514 |14966292 
GO:0048103somatic stem cell divisionISS-
GO:0010389regulation of G2/M transition of mitotic cell cycleIMP15582998 
GO:0006919caspase activationIMP12082630 
GO:0006915apoptosisIEA-
GO:0042326negative regulation of phosphorylationIDA8259215 |10208428 
GO:0033088negative regulation of immature T cell proliferation in the thymusISS-
GO:0032088negative regulation of NF-kappaB transcription factor activityIDA10353611 
GO:0030308negative regulation of cell growthIDA10208428 
GO:0031647regulation of protein stabilityISS-
GO:0030889negative regulation of B cell proliferationISS-
GO:0045736negative regulation of cyclin-dependent protein kinase activityIDA8259215 
GO:0045786negative regulation of cell cycleIEA-
GO:0051444negative regulation of ubiquitin-protein ligase activityISS-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005634nucleusIDA16243918 
GO:0005634nucleusIEA-
GO:0005654nucleoplasmIDA17110379 
GO:0005730nucleolusIDA17110379 
GO:0005737cytoplasmIDA16243918 

Section IV. Protein-protein interaction annotation

InteractorsAliases BOfficial full name BExperimentalSourcePubMed ID
ALS2CR8CARF | DKFZp667N246 | FLJ12675 | FLJ21579 | NYD-SP24amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 8-HPRD12154087 
AURKAAIK | ARK1 | AURA | AURORA2 | BTAK | MGC34538 | STK15 | STK6 | STK7aurora kinase AAffinity Capture-MSBioGRID17353931 
CCND1BCL1 | D11S287E | PRAD1 | U21B31cyclin D1Reconstituted ComplexBioGRID10580009 
CCND2KIAK0002 | MGC102758cyclin D2Reconstituted ComplexBioGRID15065884 
CCNG1CCNGcyclin G1-HPRD,BioGRID12556559 
CDK4CMM3 | MGC14458 | PSK-J3cyclin-dependent kinase 4p16 interacts with cdk4. This interaction was modeled on a demonstrated interaction between human p16 and cdk4 from an unspecified species.BIND9482104 
CDK4CMM3 | MGC14458 | PSK-J3cyclin-dependent kinase 4CDKN2A interacts with CDK4BIND11556834 
CDK4CMM3 | MGC14458 | PSK-J3cyclin-dependent kinase 4-HPRD,BioGRID9228064 
CDK4CMM3 | MGC14458 | PSK-J3cyclin-dependent kinase 4-HPRD9228064 |15232106 
CDK4CMM3 | MGC14458 | PSK-J3cyclin-dependent kinase 4p16 interacts with CDK4. This interaction was modeled on a demonstrated interaction between human p16 and CDK4 from an unspecified species.BIND10491434 
CDK4CMM3 | MGC14458 | PSK-J3cyclin-dependent kinase 4p16 interacts with cdk4.BIND8805225 
CDK6MGC59692 | PLSTIRE | STQTL11cyclin-dependent kinase 6CDKN2A interacts with CDK6BIND11556834 
CDK6MGC59692 | PLSTIRE | STQTL11cyclin-dependent kinase 6p16 interacts with CDK6. This interaction was modeled on a demonstrated interaction between human p16 and CDK6 from an unspecified species.BIND10491434 
CDK6MGC59692 | PLSTIRE | STQTL11cyclin-dependent kinase 6p16 interacts with cdk6. This interaction was modeled on a demonstrated interaction between human p16 and cdk6 from an unspecified species.BIND9482104 
CDK6MGC59692 | PLSTIRE | STQTL11cyclin-dependent kinase 6p16 interacts with cdk6.BIND8805225 
CDK6MGC59692 | PLSTIRE | STQTL11cyclin-dependent kinase 6-HPRD,BioGRID9751050 
CDKN2AIPCARF | FLJ20036CDKN2A interacting protein-HPRD12154087 
CDKN2CINK4C | p18 | p18-INK4Ccyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)-HPRD8259215 
E2F1E2F-1 | RBAP1 | RBBP3 | RBP3E2F transcription factor 1p14ARF interacts with E2F-1.BIND12082609 
E4F1E4F | MGC99614E4F transcription factor 1-HPRD,BioGRID12446718 
FKBP2FKBP-13 | PPIaseFK506 binding protein 2, 13kDaAffinity Capture-WesternBioGRID12606707 
HIF1AHIF-1alpha | HIF1 | HIF1-ALPHA | MOP1 | PASD8hypoxia-inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)p14ARF interacts with HIF-1alpha.BIND11382768 
HUWE1ARF-BP1 | HECTH9 | HSPC272 | Ib772 | KIAA0312 | LASU1 | MULE | UREB1HECT, UBA and WWE domain containing 1ARF interacts with ARF-BP1.BIND15989956 
MAPK10FLJ12099 | FLJ33785 | JNK3 | JNK3A | MGC50974 | PRKM10 | p493F12 | p54bSAPKmitogen-activated protein kinase 10CDKN2A (p16INK4a) interacts with MAPK10 (JNK3)BIND16007099 
MAPK8JNK | JNK1 | JNK1A2 | JNK21B1/2 | PRKM8 | SAPK1mitogen-activated protein kinase 8CDKN2A (p16INK4a) interacts with MAPK8 (JNK1)BIND16007099 
MCM2BM28 | CCNL1 | CDCL1 | D3S3194 | KIAA0030 | MGC10606 | MITOTIN | cdc19minichromosome maintenance complex component 2-HPRD15232106 
MDM2HDMX | MGC71221 | hdm2Mdm2 p53 binding protein homolog (mouse)-HPRD9529248 |12085228|9529249 
MDM2HDMX | MGC71221 | hdm2Mdm2 p53 binding protein homolog (mouse)p14ARF interacts with an unspecified isoform of Mdm2.BIND12582152 
MDM2HDMX | MGC71221 | hdm2Mdm2 p53 binding protein homolog (mouse)Affinity Capture-MS
Affinity Capture-Western
Reconstituted Complex
Two-hybrid		BioGRID9529248 |9529249 
|12085228 |14612427 
MDM2HDMX | MGC71221 | hdm2Mdm2 p53 binding protein homolog (mouse)Mdm2 interacts with p14ARF.BIND10822382 
MDM2HDMX | MGC71221 | hdm2Mdm2 p53 binding protein homolog (mouse)p14 interacts with MDM2.BIND15355988 
MDM2HDMX | MGC71221 | hdm2Mdm2 p53 binding protein homolog (mouse)MDM2 interacts with p14ARFBIND9653180 
MDM4DKFZp781B1423 | HDMX | MDMX | MGC132766 | MRP1Mdm4 p53 binding protein homolog (mouse)Affinity Capture-WesternBioGRID11297540 
MYCbHLHe39 | c-Mycv-myc myelocytomatosis viral oncogene homolog (avian)p14ARF interacts with c-Myc.BIND15361884 
NCOR1KIAA1047 | MGC104216 | N-CoR | TRAC1 | hCIT529I10 | hN-CoRnuclear receptor co-repressor 1NCOR1 (N-CoR) interacts with p-p14(ARF) (p14(ARF) promoter).BIND15729358 
NCOR2CTG26 | SMRT | SMRTE | SMRTE-tau | TNRC14 | TRAC-1 | TRAC1nuclear receptor co-repressor 2NCOR2 (SMRT) interacts with p-p14(ARF) (p14(ARF) promoter).BIND15729358 
PLEKHA8FAPP2 | MGC3358pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8Reconstituted ComplexBioGRID15107860 
PPP1R9BFLJ30345 | PPP1R6 | PPP1R9 | SPINO | Spnprotein phosphatase 1, regulatory (inhibitor) subunit 9B-HPRD,BioGRID11278317 
PPP1R9BFLJ30345 | PPP1R6 | PPP1R9 | SPINO | Spnprotein phosphatase 1, regulatory (inhibitor) subunit 9BSPINO interacts with p14ARF.BIND11278317 
PSMC3MGC8487 | TBP1proteasome (prosome, macropain) 26S subunit, ATPase, 3p14ARF interacts with TBP-1.BIND14665636 
RPL11GIG34ribosomal protein L11Affinity Capture-WesternBioGRID14612427 
SERTAD1SEI1 | TRIP-Br1SERTA domain containing 1-HPRD,BioGRID10580009 |15065884 
TP53FLJ92943 | LFS1 | TRP53 | p53tumor protein p53Affinity Capture-WesternBioGRID9529249 |12446718 
|14612427 
UBE2AHHR6A | RAD6A | UBC2ubiquitin-conjugating enzyme E2A (RAD6 homolog)Affinity Capture-WesternBioGRID12640129 
WRNDKFZp686C2056 | RECQ3 | RECQL2 | RECQL3Werner syndromep14 interacts with WRN.BIND15355988 
YY1DELTA | INO80S | NF-E1 | UCRBP | YIN-YANG-1YY1 transcription factorYY1 interacts with p14ARF.BIND15210108 
ZNF410APA-1 | APA1zinc finger protein 410-HPRD12370286 


Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG CELL CYCLE 12884All SZGR 2.0 genes in this pathway
KEGG P53 SIGNALING PATHWAY 6945All SZGR 2.0 genes in this pathway
KEGG PATHWAYS IN CANCER 328259All SZGR 2.0 genes in this pathway
KEGG PANCREATIC CANCER 7056All SZGR 2.0 genes in this pathway
KEGG GLIOMA 6556All SZGR 2.0 genes in this pathway
KEGG MELANOMA 7157All SZGR 2.0 genes in this pathway
KEGG BLADDER CANCER 4233All SZGR 2.0 genes in this pathway
KEGG CHRONIC MYELOID LEUKEMIA 7359All SZGR 2.0 genes in this pathway
KEGG NON SMALL CELL LUNG CANCER 5447All SZGR 2.0 genes in this pathway
BIOCARTA G1 PATHWAY 2821All SZGR 2.0 genes in this pathway
BIOCARTA CTCF PATHWAY 2318All SZGR 2.0 genes in this pathway
BIOCARTA CELLCYCLE PATHWAY 2315All SZGR 2.0 genes in this pathway
BIOCARTA ARF PATHWAY 1713All SZGR 2.0 genes in this pathway
SIG PIP3 SIGNALING IN CARDIAC MYOCTES 6754All SZGR 2.0 genes in this pathway
ST INTEGRIN SIGNALING PATHWAY 8262All SZGR 2.0 genes in this pathway
SA G1 AND S PHASES 1510All SZGR 2.0 genes in this pathway
SIG INSULIN RECEPTOR PATHWAY IN CARDIAC MYOCYTES 5141All SZGR 2.0 genes in this pathway
SIG PIP3 SIGNALING IN B LYMPHOCYTES 3631All SZGR 2.0 genes in this pathway
SA REG CASCADE OF CYCLIN EXPR 137All SZGR 2.0 genes in this pathway
ST PHOSPHOINOSITIDE 3 KINASE PATHWAY 3729All SZGR 2.0 genes in this pathway
PID E2F PATHWAY 7448All SZGR 2.0 genes in this pathway
PID AR PATHWAY 6146All SZGR 2.0 genes in this pathway
PID FRA PATHWAY 3728All SZGR 2.0 genes in this pathway
PID MYC PATHWAY 2522All SZGR 2.0 genes in this pathway
PID AP1 PATHWAY 7060All SZGR 2.0 genes in this pathway
PID FOXM1 PATHWAY 4030All SZGR 2.0 genes in this pathway
PID HIF1A PATHWAY 1912All SZGR 2.0 genes in this pathway
PID CMYB PATHWAY 8461All SZGR 2.0 genes in this pathway
PID BETA CATENIN NUC PATHWAY 8060All SZGR 2.0 genes in this pathway
PID DELTA NP63 PATHWAY 4734All SZGR 2.0 genes in this pathway
PID TAP63 PATHWAY 5440All SZGR 2.0 genes in this pathway
PID P53 REGULATION PATHWAY 5950All SZGR 2.0 genes in this pathway
PID RB 1PATHWAY 6546All SZGR 2.0 genes in this pathway
REACTOME CELL CYCLE 421253All SZGR 2.0 genes in this pathway
REACTOME CELL CYCLE MITOTIC 325185All SZGR 2.0 genes in this pathway
REACTOME G1 PHASE 3823All SZGR 2.0 genes in this pathway
REACTOME MITOTIC G1 G1 S PHASES 13779All SZGR 2.0 genes in this pathway
PYEON HPV POSITIVE TUMORS UP 9847All SZGR 2.0 genes in this pathway
CORRE MULTIPLE MYELOMA UP 7445All SZGR 2.0 genes in this pathway
BORCZUK MALIGNANT MESOTHELIOMA DN 10459All SZGR 2.0 genes in this pathway
SLEBOS HEAD AND NECK CANCER WITH HPV UP 8443All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA ANAPLASTIC UP 722443All SZGR 2.0 genes in this pathway
PROVENZANI METASTASIS UP 194112All SZGR 2.0 genes in this pathway
CASTELLANO NRAS TARGETS DN 1414All SZGR 2.0 genes in this pathway
CAIRO PML TARGETS BOUND BY MYC DN 1412All SZGR 2.0 genes in this pathway
TAKADA GASTRIC CANCER COPY NUMBER DN 2915All SZGR 2.0 genes in this pathway
BUSA SAM68 TARGETS UP 76All SZGR 2.0 genes in this pathway
ROVERSI GLIOMA COPY NUMBER DN 5437All 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
ROSTY CERVICAL CANCER PROLIFERATION CLUSTER 14073All SZGR 2.0 genes in this pathway
HONRADO BREAST CANCER BRCA1 VS BRCA2 1812All SZGR 2.0 genes in this pathway
DAWSON METHYLATED IN LYMPHOMA TCL1 5945All SZGR 2.0 genes in this pathway
OHM METHYLATED IN ADULT CANCERS 2723All SZGR 2.0 genes in this pathway
OHM EMBRYONIC CARCINOMA DN 86All SZGR 2.0 genes in this pathway
FRIDMAN SENESCENCE UP 7760All SZGR 2.0 genes in this pathway
FRIDMAN IMMORTALIZATION DN 3424All SZGR 2.0 genes in this pathway
RICKMAN HEAD AND NECK CANCER B 4822All SZGR 2.0 genes in this pathway
GOTZMANN EPITHELIAL TO MESENCHYMAL TRANSITION DN 206136All SZGR 2.0 genes in this pathway
GEORGES TARGETS OF MIR192 AND MIR215 893528All SZGR 2.0 genes in this pathway
TCGA GLIOBLASTOMA COPY NUMBER DN 3121All SZGR 2.0 genes in this pathway
DING LUNG CANCER MUTATED SIGNIFICANTLY 2622All SZGR 2.0 genes in this pathway
SHIPP DLBCL CURED VS FATAL DN 4530All SZGR 2.0 genes in this pathway
SMITH TERT TARGETS UP 14591All SZGR 2.0 genes in this pathway
TENEDINI MEGAKARYOCYTE MARKERS 6648All SZGR 2.0 genes in this pathway
SUZUKI RESPONSE TO TSA AND DECITABINE 1A 2316All SZGR 2.0 genes in this pathway
SATO SILENCED EPIGENETICALLY IN PANCREATIC CANCER 4930All SZGR 2.0 genes in this pathway
YIH RESPONSE TO ARSENITE C3 3624All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 9 9259All SZGR 2.0 genes in this pathway
BILD E2F3 ONCOGENIC SIGNATURE 246153All SZGR 2.0 genes in this pathway
LOPES METHYLATED IN COLON CANCER UP 2720All SZGR 2.0 genes in this pathway
LOPES METHYLATED IN COLON CANCER DN 2826All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS SILENCED BY METHYLATION DN 281179All SZGR 2.0 genes in this pathway
LIN MELANOMA COPY NUMBER DN 4134All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER WITH H3K27ME3 DN 228114All SZGR 2.0 genes in this pathway
HOQUE METHYLATED IN CANCER 5645All SZGR 2.0 genes in this pathway
SMID BREAST CANCER RELAPSE IN BONE DN 315197All SZGR 2.0 genes in this pathway
SMID BREAST CANCER LUMINAL B DN 564326All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL UP 648398All SZGR 2.0 genes in this pathway
ZHENG GLIOBLASTOMA PLASTICITY UP 250168All SZGR 2.0 genes in this pathway
GRESHOCK CANCER COPY NUMBER UP 323240All SZGR 2.0 genes in this pathway
BOHN PRIMARY IMMUNODEFICIENCY SYNDROM DN 4031All SZGR 2.0 genes in this pathway
AGUIRRE PANCREATIC CANCER COPY NUMBER UP 298174All SZGR 2.0 genes in this pathway
SHEDDEN LUNG CANCER POOR SURVIVAL A6 456285All SZGR 2.0 genes in this pathway
MIKKELSEN PARTIALLY REPROGRAMMED TO PLURIPOTENCY 106All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K4ME3 AND H3K27ME3 1069729All SZGR 2.0 genes in this pathway
YAMASHITA LIVER CANCER STEM CELL UP 4738All SZGR 2.0 genes in this pathway
YAMASHITA LIVER CANCER STEM CELL DN 7651All SZGR 2.0 genes in this pathway
LI PROSTATE CANCER EPIGENETIC 3022All SZGR 2.0 genes in this pathway
PYEON CANCER HEAD AND NECK VS CERVICAL UP 19395All SZGR 2.0 genes in this pathway
LI INDUCED T TO NATURAL KILLER UP 307182All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS GROWING 243155All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS CONFLUENT 567365All SZGR 2.0 genes in this pathway
DUTERTRE ESTRADIOL RESPONSE 24HR DN 505328All SZGR 2.0 genes in this pathway
PURBEY TARGETS OF CTBP1 AND SATB1 DN 180116All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION UP 570339All SZGR 2.0 genes in this pathway
RAO BOUND BY SALL4 ISOFORM A 182108All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 1ST EGF PULSE ONLY 1839928All SZGR 2.0 genes in this pathway