Summary ?
GeneID5591
SymbolPRKDC
SynonymsDNA-PKcs|DNAPK|DNPK1|HYRC|HYRC1|IMD26|XRCC7|p350
Descriptionprotein kinase, DNA-activated, catalytic polypeptide
ReferenceMIM:600899|HGNC:HGNC:9413|Ensembl:ENSG00000253729|HPRD:02941|Vega:OTTHUMG00000164239
Gene typeprotein-coding
Map location8q11
Pascal p-value0.305
Sherlock p-value0.681
Fetal beta0.866
DMG1 (# studies)
eGeneMyers' cis & trans
SupportG2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:vanEijk_2014Genome-wide DNA methylation analysisThis dataset includes 432 differentially methylated CpG sites corresponding to 391 unique transcripts between schizophrenia patients (n=260) and unaffected controls (n=250). 1
DNM:McCarthy_2014Whole Exome Sequencing analysisWhole exome sequencing of 57 trios with sporadic or familial schizophrenia.
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 1 
NetworkShortest path distance of core genes in the Human protein-protein interaction networkContribution to shortest path in PPI network: 0.0381 

Section I. Genetics and epigenetics annotation

@DNM table

GeneChromosomePositionRefAltTranscriptAA changeMutation typeSiftCG46TraitStudy
PRKDCchr848868449UNKNOWNNAsynonymous SNVSchizophreniaDNM:McCarthy_2014

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg16104446848873951PRKDC0.005-7.73DMG:vanEijk_2014

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs7132043chr1280968399PRKDC55910.07trans

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
LRRC240.790.74
LRFN40.750.75
COMTD10.740.68
AC006273.10.730.72
ZNF7680.730.77
FAM171A20.730.73
MACROD10.730.69
GPR172A0.730.74
MFSD100.730.74
AC009133.10.720.69
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
S100B-0.51-0.60
AF347015.27-0.49-0.57
C5orf53-0.49-0.55
ACOT13-0.48-0.53
PIR-0.48-0.56
COPZ2-0.47-0.54
AF347015.33-0.47-0.56
LACTB2-0.47-0.53
CSRP1-0.47-0.53
SLCO1A2-0.47-0.58

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0003677DNA bindingIEA-
GO:0005515protein bindingIPI9442054 
GO:0005524ATP bindingIEA-
GO:0004677DNA-dependent protein kinase activityIDA15194694 
GO:0016740transferase activityIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0007420brain developmentIEABrain (GO term level: 7)-
GO:0001756somitogenesisIEA-
GO:0000723telomere maintenanceIEA-
GO:0002328pro-B cell differentiationIEA-
GO:0006303double-strand break repair via nonhomologous end joiningIEA-
GO:0006310DNA recombinationIEA-
GO:0006464protein modification processTAS7671312 
GO:0010332response to gamma radiationIEA-
GO:0007507heart developmentIEA-
GO:0006915apoptosisIEA-
GO:0018105peptidyl-serine phosphorylationIDA15194694 
GO:0033077T cell differentiation in the thymusIEA-
GO:0033153T cell receptor V(D)J recombinationIEA-
GO:0033152immunoglobulin V(D)J recombinationIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005634nucleusIEA-
GO:0005654nucleoplasmEXP12023295 |12065431 
GO:0005958DNA-dependent protein kinase complexIDA15194694 

Section IV. Protein-protein interaction annotation

InteractorsAliases BOfficial full name BExperimentalSourcePubMed ID
ABL1ABL | JTK7 | bcr/abl | c-ABL | p150 | v-ablc-abl oncogene 1, receptor tyrosine kinase-HPRD,BioGRID9312071 
AKT1AKT | MGC99656 | PKB | PKB-ALPHA | PRKBA | RAC | RAC-ALPHAv-akt murine thymoma viral oncogene homolog 1DNA-PKcs interacts with Akt1.BIND15678105 
AKT2PKBB | PKBBETA | PRKBB | RAC-BETAv-akt murine thymoma viral oncogene homolog 2Biochemical ActivityBioGRID16221682 
AP1B1ADTB1 | AP105A | BAM22 | CLAPB2adaptor-related protein complex 1, beta 1 subunitProtein-peptideBioGRID10608806 
ARAIS | DHTR | HUMARA | KD | NR3C4 | SBMA | SMAX1 | TFMandrogen receptorAffinity Capture-MSBioGRID15640154 
ATMAT1 | ATA | ATC | ATD | ATDC | ATE | DKFZp781A0353 | MGC74674 | TEL1 | TELO1ataxia telangiectasia mutated-HPRD,BioGRID10464290 
BRCA1BRCAI | BRCC1 | IRIS | PSCP | RNF53breast cancer 1, early onsetProtein-peptideBioGRID10608806 
C1DMGC12261 | MGC14659 | SUNCORnuclear DNA-binding protein-HPRD,BioGRID9679063 
CHEK1CHK1CHK1 checkpoint homolog (S. pombe)Protein-peptide
Reconstituted Complex
BioGRID10608806 |12756247 
CHUKIKBKA | IKK-alpha | IKK1 | IKKA | NFKBIKA | TCF16conserved helix-loop-helix ubiquitous kinase-HPRD,BioGRID9632806 
CIB1CIB | KIP | KIP1 | SIP2-28calcium and integrin binding 1 (calmyrin)-HPRD,BioGRID9372844 
DCLRE1CA-SCID | DCLREC1C | FLJ11360 | FLJ36438 | RS-SCID | SCIDA | SNM1CDNA cross-link repair 1C (PSO2 homolog, S. cerevisiae)Affinity Capture-Western
Biochemical Activity
Reconstituted Complex
BioGRID11955432 
E4F1E4F | MGC99614E4F transcription factor 1Protein-peptideBioGRID10608806 
EIF2S2DKFZp686L18198 | EIF2 | EIF2B | EIF2beta | MGC8508eukaryotic translation initiation factor 2, subunit 2 beta, 38kDa-HPRD,BioGRID9442054 
HOXC4HOX3 | HOX3E | cp19homeobox C4-HPRD11279128 
HSF1HSTF1heat shock transcription factor 1in vitroBioGRID9325337 
IKBKBFLJ40509 | IKK-beta | IKK2 | IKKB | MGC131801 | NFKBIKBinhibitor of kappa light polypeptide gene enhancer in B-cells, kinase betaBiochemical ActivityBioGRID9632806 
ILF2MGC8391 | NF45 | PRO3063interleukin enhancer binding factor 2, 45kDa-HPRD,BioGRID9442054 
ILF3CBTF | DRBF | DRBP76 | MMP4 | MPHOSPH4 | MPP4 | NF-AT-90 | NF110 | NF90 | NFAR | NFAR-1 | NFAR2 | TCP110 | TCP80interleukin enhancer binding factor 3, 90kDa-HPRD,BioGRID9442054 
KAT2AGCN5 | GCN5L2 | MGC102791 | PCAF-b | hGCN5K(lysine) acetyltransferase 2ABiochemical ActivityBioGRID9488450 
LIG4-ligase IV, DNA, ATP-dependentProtein-peptideBioGRID10608806 
LYNFLJ26625 | JTK8v-yes-1 Yamaguchi sarcoma viral related oncogene homolog-HPRD,BioGRID9748231 
MAPK8JNK | JNK1 | JNK1A2 | JNK21B1/2 | PRKM8 | SAPK1mitogen-activated protein kinase 8-HPRD,BioGRID11749722 
MAPK9JNK-55 | JNK2 | JNK2A | JNK2ALPHA | JNK2B | JNK2BETA | PRKM9 | SAPK | p54a | p54aSAPKmitogen-activated protein kinase 9Biochemical ActivityBioGRID11749722 
MRE11AATLD | HNGS1 | MRE11 | MRE11BMRE11 meiotic recombination 11 homolog A (S. cerevisiae)Protein-peptideBioGRID10608806 
NBNAT-V1 | AT-V2 | ATV | FLJ10155 | MGC87362 | NBS | NBS1 | P95nibrinNBS1 interacts with PRKDC (DNA-PKc).BIND15758953 
NCF1FLJ79451 | NCF1A | NOXO2 | SH3PXD1A | p47phoxneutrophil cytosolic factor 1Biochemical ActivityBioGRID9914162 
NCF2FLJ93058 | NCF-2 | NOXA2 | P67-PHOX | P67PHOXneutrophil cytosolic factor 2Biochemical ActivityBioGRID9914162 
NCF4MGC3810 | NCF | P40PHOX | SH3PXD4neutrophil cytosolic factor 4, 40kDaBiochemical ActivityBioGRID9914162 
NCOA6AIB3 | ANTP | ASC2 | HOX1.1 | HOXA7 | KIAA0181 | NRC | PRIP | RAP250 | TRBPnuclear receptor coactivator 6Affinity Capture-MS
Biochemical Activity
BioGRID10823961 
PARP1ADPRT | ADPRT1 | PARP | PARP-1 | PPOL | pADPRT-1poly (ADP-ribose) polymerase 1-HPRD9398855 
PCNAMGC8367proliferating cell nuclear antigen-HPRD,BioGRID12171929 
PCNAMGC8367proliferating cell nuclear antigenPRKDC is a PCNA-binding proteinBIND12171929 
PRKCDMAY1 | MGC49908 | PKCD | nPKC-deltaprotein kinase C, delta-HPRD9774685 
PTSFLJ97081 | PTPS6-pyruvoyltetrahydropterin synthaseProtein-peptideBioGRID10608806 
RAD17CCYC | FLJ41520 | HRAD17 | R24L | RAD17SP | RAD24RAD17 homolog (S. pombe)Protein-peptideBioGRID10608806 
RBBP8CTIP | RIMretinoblastoma binding protein 8Protein-peptideBioGRID10608806 
RPA1HSSB | REPA1 | RF-A | RP-A | RPA70replication protein A1, 70kDa-HPRD,BioGRID10064605 
RPA2REPA2 | RPA32replication protein A2, 32kDaDNA-PKcs interacts with RPA2.BIND11000264 
RPA2REPA2 | RPA32replication protein A2, 32kDa-HPRD,BioGRID10064605 |11731442 
TP53FLJ92943 | LFS1 | TRP53 | p53tumor protein p53-HPRD10470151 
TP53FLJ92943 | LFS1 | TRP53 | p53tumor protein p53Biochemical Activity
Protein-peptide
BioGRID9679063 |10608806 
|12756247 
TRADDHs.89862 | MGC11078TNFRSF1A-associated via death domain-HPRD14743216 
WRNDKFZp686C2056 | RECQ3 | RECQL2 | RECQL3Werner syndrome-HPRD,BioGRID11889123 
XRCC4-X-ray repair complementing defective repair in Chinese hamster cells 4-HPRD9430729 
XRCC5FLJ39089 | KARP-1 | KARP1 | KU80 | KUB2 | Ku86 | NFIVX-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)-HPRD10207052 |10446239 
XRCC5FLJ39089 | KARP-1 | KARP1 | KU80 | KUB2 | Ku86 | NFIVX-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)XRCC5 (Ku80) interacts with PRKDC (DNA-PKc).BIND15758953 
XRCC5FLJ39089 | KARP-1 | KARP1 | KU80 | KUB2 | Ku86 | NFIVX-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)Affinity Capture-Western
in vitro
in vivo
Reconstituted Complex
BioGRID9312071 |10446239 
|12393188 
XRCC6CTC75 | CTCBF | G22P1 | KU70 | ML8 | TLAAX-ray repair complementing defective repair in Chinese hamster cells 6-HPRD9312071 |10446239 
|11279128 
XRCC6CTC75 | CTCBF | G22P1 | KU70 | ML8 | TLAAX-ray repair complementing defective repair in Chinese hamster cells 6Affinity Capture-Western
in vitro
in vivo
BioGRID10064605 |10446239 


Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG NON HOMOLOGOUS END JOINING 148All SZGR 2.0 genes in this pathway
KEGG CELL CYCLE 12884All SZGR 2.0 genes in this pathway
BIOCARTA G2 PATHWAY 2420All SZGR 2.0 genes in this pathway
BIOCARTA FAS PATHWAY 3022All SZGR 2.0 genes in this pathway
BIOCARTA HIVNEF PATHWAY 5843All SZGR 2.0 genes in this pathway
BIOCARTA TNFR1 PATHWAY 2921All SZGR 2.0 genes in this pathway
PID DNA PK PATHWAY 1610All SZGR 2.0 genes in this pathway
PID AR PATHWAY 6146All SZGR 2.0 genes in this pathway
PID PI3KCI AKT PATHWAY 3530All SZGR 2.0 genes in this pathway
PID BARD1 PATHWAY 2919All SZGR 2.0 genes in this pathway
REACTOME DOUBLE STRAND BREAK REPAIR 2414All SZGR 2.0 genes in this pathway
REACTOME DNA REPAIR 11259All SZGR 2.0 genes in this pathway
ONKEN UVEAL MELANOMA UP 783507All SZGR 2.0 genes in this pathway
SENGUPTA NASOPHARYNGEAL CARCINOMA UP 294178All SZGR 2.0 genes in this pathway
GAZDA DIAMOND BLACKFAN ANEMIA PROGENITOR DN 6642All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP 1382904All SZGR 2.0 genes in this pathway
DEURIG T CELL PROLYMPHOCYTIC LEUKEMIA UP 368234All SZGR 2.0 genes in this pathway
BORCZUK MALIGNANT MESOTHELIOMA UP 305185All SZGR 2.0 genes in this pathway
GAL LEUKEMIC STEM CELL UP 13378All SZGR 2.0 genes in this pathway
BASAKI YBX1 TARGETS UP 290177All SZGR 2.0 genes in this pathway
RHEIN ALL GLUCOCORTICOID THERAPY DN 362238All SZGR 2.0 genes in this pathway
KINSEY TARGETS OF EWSR1 FLII FUSION UP 1278748All SZGR 2.0 genes in this pathway
BIDUS METASTASIS UP 214134All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA DN 1375806All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA POORLY DIFFERENTIATED UP 633376All SZGR 2.0 genes in this pathway
ENK UV RESPONSE KERATINOCYTE DN 485334All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN DN 17811082All SZGR 2.0 genes in this pathway
OUELLET OVARIAN CANCER INVASIVE VS LMP UP 11785All SZGR 2.0 genes in this pathway
MISSIAGLIA REGULATED BY METHYLATION DN 12267All SZGR 2.0 genes in this pathway
WAKASUGI HAVE ZNF143 BINDING SITES 5833All SZGR 2.0 genes in this pathway
FARMER BREAST CANCER CLUSTER 2 3317All SZGR 2.0 genes in this pathway
PATIL LIVER CANCER 747453All SZGR 2.0 genes in this pathway
MOHANKUMAR TLX1 TARGETS UP 414287All SZGR 2.0 genes in this pathway
GRUETZMANN PANCREATIC CANCER UP 358245All SZGR 2.0 genes in this pathway
PUJANA BREAST CANCER LIT INT NETWORK 10173All SZGR 2.0 genes in this pathway
PUJANA XPRSS INT NETWORK 168103All 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
PUJANA ATM PCC NETWORK 1442892All SZGR 2.0 genes in this pathway
PUJANA CHEK2 PCC NETWORK 779480All SZGR 2.0 genes in this pathway
PUJANA BRCA CENTERED NETWORK 11772All SZGR 2.0 genes in this pathway
BENPORATH MYC MAX TARGETS 775494All SZGR 2.0 genes in this pathway
KAUFFMANN DNA REPAIR GENES 230137All SZGR 2.0 genes in this pathway
TARTE PLASMA CELL VS PLASMABLAST DN 309206All SZGR 2.0 genes in this pathway
FERNANDEZ BOUND BY MYC 182116All SZGR 2.0 genes in this pathway
REN BOUND BY E2F 6140All SZGR 2.0 genes in this pathway
ZHAN MULTIPLE MYELOMA SUBGROUPS 3020All SZGR 2.0 genes in this pathway
MOREAUX B LYMPHOCYTE MATURATION BY TACI DN 7345All SZGR 2.0 genes in this pathway
MOREAUX MULTIPLE MYELOMA BY TACI DN 172107All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS EARLY PROGENITOR 532309All SZGR 2.0 genes in this pathway
LEE AGING NEOCORTEX DN 8049All SZGR 2.0 genes in this pathway
MARSON BOUND BY E2F4 UNSTIMULATED 728415All SZGR 2.0 genes in this pathway
FUJII YBX1 TARGETS DN 202132All SZGR 2.0 genes in this pathway
MITSIADES RESPONSE TO APLIDIN DN 249165All SZGR 2.0 genes in this pathway
SMID BREAST CANCER RELAPSE IN BONE DN 315197All SZGR 2.0 genes in this pathway
BONOME OVARIAN CANCER SURVIVAL OPTIMAL DEBULKING 246152All SZGR 2.0 genes in this pathway
BOCHKIS FOXA2 TARGETS 425261All SZGR 2.0 genes in this pathway
GRADE COLON CANCER UP 871505All SZGR 2.0 genes in this pathway
GRADE COLON AND RECTAL CANCER UP 285167All SZGR 2.0 genes in this pathway
BLUM RESPONSE TO SALIRASIB DN 342220All SZGR 2.0 genes in this pathway
FIRESTEIN PROLIFERATION 175125All SZGR 2.0 genes in this pathway
SHEDDEN LUNG CANCER POOR SURVIVAL A6 456285All SZGR 2.0 genes in this pathway
DING LUNG CANCER BY MUTATION RATE 2018All SZGR 2.0 genes in this pathway
BOYAULT LIVER CANCER SUBCLASS G123 UP 4521All SZGR 2.0 genes in this pathway
FOURNIER ACINAR DEVELOPMENT LATE 2 277172All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA CLASSES UP 605377All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC 1103714All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS SENESCENT 572352All SZGR 2.0 genes in this pathway
WIERENGA PML INTERACTOME 4223All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 3 DN 918550All SZGR 2.0 genes in this pathway
ABRAMSON INTERACT WITH AIRE 4533All SZGR 2.0 genes in this pathway