Summary?
GeneID 5591
Symbol PRKDC
Synonyms DNA-PKcs|DNAPK|DNPK1|HYRC|HYRC1|IMD26|XRCC7|p350
Description protein kinase, DNA-activated, catalytic polypeptide
Reference MIM:600899|HGNC:HGNC:9413|Ensembl:ENSG00000253729|HPRD:02941|Vega:OTTHUMG00000164239
Gene type protein-coding
Map location 8q11
Pascal p-value 0.305
Sherlock p-value 0.681
Fetal beta 0.866
DMG 1 (# studies)
eGene Myers' cis & trans
Support G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS

Gene in Data Sources
Gene set name Method of gene set Description Info
CV:PGCnp Genome-wide Association Study GWAS
DMG:vanEijk_2014 Genome-wide DNA methylation analysis This 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_2014 Whole Exome Sequencing analysis Whole exome sequencing of 57 trios with sporadic or familial schizophrenia.
GO_Annotation Mapping neuro-related keywords to Gene Ontology annotations Hits with neuro-related keywords: 1
Network Shortest path distance of core genes in the Human protein-protein interaction network Contribution to shortest path in PPI network: 0.0381

Section I. Genetics and epigenetics annotation

@DNM table

Gene Chromosome Position Ref Alt Transcript AA change Mutation type Sift CG46 Trait Study
PRKDC chr8 48868449 UNKNOWN NA synonymous SNV Schizophrenia DNM:McCarthy_2014

@Differentially methylated gene

Probe Chromosome Position Nearest gene P (dis) Beta (dis) FDR (dis) Study
cg16104446 8 48873951 PRKDC 0.005 -7.73 DMG:vanEijk_2014

@eQTLannotation

SNP ID Chromosome Position eGene Gene Entrez ID pvalue qvalue TSS distance eQTLtype
rs7132043 chr12 80968399 PRKDC 5591 0.07 trans

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
Gene Pearson's Correlation Spearman's Correlation
LRRC24 0.79 0.74
LRFN4 0.75 0.75
COMTD1 0.74 0.68
AC006273.1 0.73 0.72
ZNF768 0.73 0.77
FAM171A2 0.73 0.73
MACROD1 0.73 0.69
GPR172A 0.73 0.74
MFSD10 0.73 0.74
AC009133.1 0.72 0.69
Top 10 negatively co-expressed genes
Gene Pearson'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 function GO term Evidence Neuro keywords PubMed ID
GO:0003677 DNA binding IEA -
GO:0005515 protein binding 新闻学会 9442054
GO:0005524 ATP binding IEA -
GO:0004677 DNA-dependent protein kinase activity IDA 15194694
GO:0016740 transferase activity IEA -
Biological process GO term Evidence Neuro keywords PubMed ID
GO:0007420 brain development IEA Brain (GO term level: 7) -
GO:0001756 somitogenesis IEA -
GO:0000723 telomere maintenance IEA -
GO:0002328 pro-B cell differentiation IEA -
GO:0006303 double-strand break repair via nonhomologous end joining IEA -
GO:0006310 DNA recombination IEA -
GO:0006464 蛋白质莫dification process TAS 7671312
GO:0010332 response to gamma radiation IEA -
GO:0007507 heart development IEA -
GO:0006915 apoptosis IEA -
GO:0018105 peptidyl-serine phosphorylation IDA 15194694
GO:0033077 T cell differentiation in the thymus IEA -
GO:0033153 T cell receptor V(D)J recombination IEA -
GO:0033152 immunoglobulin V(D)J recombination IEA -
Cellular component GO term Evidence Neuro keywords PubMed ID
GO:0005634 nucleus IEA -
GO:0005654 nucleoplasm EXP 12023295|12065431
GO:0005958 DNA-dependent protein kinase complex IDA 15194694

Section IV. Protein-protein interaction annotation

Interactors Aliases B Official full name B Experimental Source PubMed ID
ABL1 ABL | JTK7 | bcr/abl | c-ABL | p150 | v-abl c-abl oncogene 1, receptor tyrosine kinase - HPRD,BioGRID 9312071
AKT1 AKT | MGC99656 | PKB | PKB-ALPHA | PRKBA | RAC | RAC-ALPHA v-akt murine thymoma viral oncogene homolog 1 DNA-PKcs interacts with Akt1. BIND 15678105
AKT2 PKBB | PKBBETA | PRKBB | RAC-BETA v-akt murine thymoma viral oncogene homolog 2 Biochemical Activity BioGRID 16221682
AP1B1 ADTB1 | AP105A | BAM22 | CLAPB2 adaptor-related protein complex 1, beta 1 subunit Protein-peptide BioGRID 10608806
AR AIS | DHTR | HUMARA | KD | NR3C4 | SBMA | SMAX1 |TFM androgen receptor Affinity Capture-MS BioGRID 15640154
ATM AT1 | ATA | ATC | ATD | ATDC | ATE | DKFZp781A0353 | MGC74674 | TEL1 | TELO1 ataxia telangiectasia mutated - HPRD,BioGRID 10464290
BRCA1 BRCAI | BRCC1 | IRIS | PSCP | RNF53 breast cancer 1, early onset Protein-peptide BioGRID 10608806
C1D MGC12261 | MGC14659 | SUNCOR nuclear DNA-binding protein - HPRD,BioGRID 9679063
CHEK1 CHK1 CHK1 checkpoint homolog (S. pombe) Protein-peptide
Reconstituted Complex
BioGRID 10608806|12756247
CHUK IKBKA | IKK-alpha | IKK1 | IKKA | NFKBIKA | TCF16 conserved helix-loop-helix ubiquitous kinase - HPRD,BioGRID 9632806
CIB1 CIB | KIP | KIP1 | SIP2-28 calcium and integrin binding 1 (calmyrin) - HPRD,BioGRID 9372844
DCLRE1C A-SCID | DCLREC1C | FLJ11360 | FLJ36438 | RS-SCID | SCIDA | SNM1C DNA cross-link repair 1C (PSO2 homolog, S. cerevisiae) Affinity Capture-Western
Biochemical Activity
Reconstituted Complex
BioGRID 11955432
E4F1 E4F | MGC99614 E4F transcription factor 1 Protein-peptide BioGRID 10608806
EIF2S2 DKFZp686L18198 | EIF2 | EIF2B | EIF2beta | MGC8508 eukaryotic translation initiation factor 2, subunit 2 beta, 38kDa - HPRD,BioGRID 9442054
HOXC4 HOX3 | HOX3E | cp19 homeobox C4 - HPRD 11279128
HSF1 HSTF1 heat shock transcription factor 1 in vitro BioGRID 9325337
IKBKB FLJ40509 | IKK-beta | IKK2 | IKKB | MGC131801 | NFKBIKB inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta Biochemical Activity BioGRID 9632806
ILF2 MGC8391 | NF45 | PRO3063 interleukin enhancer binding factor 2, 45kDa - HPRD,BioGRID 9442054
ILF3 CBTF | DRBF | DRBP76 | MMP4 | MPHOSPH4 | MPP4 | NF-AT-90 | NF110 | NF90 | NFAR | NFAR-1 | NFAR2 | TCP110 | TCP80 interleukin enhancer binding factor 3, 90kDa - HPRD,BioGRID 9442054
KAT2A GCN5 | GCN5L2 | MGC102791 | PCAF-b | hGCN5 K(lysine) acetyltransferase 2A Biochemical Activity BioGRID 9488450
LIG4 - ligase IV, DNA, ATP-dependent Protein-peptide BioGRID 10608806
LYN FLJ26625 | JTK8 v-yes-1 Yamaguchi sarcoma viral related oncogene homolog - HPRD,BioGRID 9748231
MAPK8 JNK | JNK1 | JNK1A2 | JNK21B1/2 | PRKM8 | SAPK1 mitogen-activated protein kinase 8 - HPRD,BioGRID 11749722
MAPK9 JNK-55 | JNK2 | JNK2A | JNK2ALPHA | JNK2B | JNK2BETA | PRKM9 | SAPK | p54a | p54aSAPK mitogen-activated protein kinase 9 Biochemical Activity BioGRID 11749722
MRE11A ATLD | HNGS1 | MRE11 | MRE11B MRE11 meiotic recombination 11 homolog A (S. cerevisiae) Protein-peptide BioGRID 10608806
NBN AT-V1 | AT-V2 | ATV | FLJ10155 | MGC87362 | NBS | NBS1 | P95 nibrin NBS1 interacts with PRKDC (DNA-PKc). BIND 15758953
NCF1 FLJ79451 | NCF1A | NOXO2 | SH3PXD1A | p47phox neutrophil cytosolic factor 1 Biochemical Activity BioGRID 9914162
NCF2 FLJ93058 | NCF-2 | NOXA2 | P67-PHOX | P67PHOX neutrophil cytosolic factor 2 Biochemical Activity BioGRID 9914162
NCF4 MGC3810 | NCF | P40PHOX | SH3PXD4 neutrophil cytosolic factor 4, 40kDa Biochemical Activity BioGRID 9914162
NCOA6 AIB3 | ANTP | ASC2 | HOX1.1 | HOXA7 | KIAA0181 | NRC | PRIP | RAP250 | TRBP nuclear receptor coactivator 6 Affinity Capture-MS
Biochemical Activity
BioGRID 10823961
PARP1 ADPRT | ADPRT1 | PARP | PARP-1 | PPOL | pADPRT-1 poly (ADP-ribose) polymerase 1 - HPRD 9398855
PCNA MGC8367 proliferating cell nuclear antigen - HPRD,BioGRID 12171929
PCNA MGC8367 proliferating cell nuclear antigen PRKDC is a PCNA-binding protein BIND 12171929
PRKCD MAY1 | MGC49908 | PKCD | nPKC-delta protein kinase C, delta - HPRD 9774685
PTS FLJ97081 | PTPS 6-pyruvoyltetrahydropterin synthase Protein-peptide BioGRID 10608806
RAD17 CCYC | FLJ41520 | HRAD17 | R24L | RAD17SP | RAD24 RAD17 homolog (S. pombe) Protein-peptide BioGRID 10608806
RBBP8 CTIP | RIM retinoblastoma binding protein 8 Protein-peptide BioGRID 10608806
RPA1 HSSB | REPA1 | RF-A | RP-A | RPA70 replication protein A1, 70kDa - HPRD,BioGRID 10064605
RPA2 REPA2 | RPA32 复制蛋白A2, 32 kda DNA-PKcs interacts with RPA2. BIND 11000264
RPA2 REPA2 | RPA32 复制蛋白A2, 32 kda - HPRD,BioGRID 10064605|11731442
TP53 FLJ92943 | LFS1 | TRP53 | p53 tumor protein p53 - HPRD 10470151
TP53 FLJ92943 | LFS1 | TRP53 | p53 tumor protein p53 Biochemical Activity
Protein-peptide
BioGRID 9679063|10608806
|12756247
TRADD Hs.89862 | MGC11078 TNFRSF1A-associated via death domain - HPRD 14743216
WRN DKFZp686C2056 | RECQ3 | RECQL2 | RECQL3 Werner syndrome - HPRD,BioGRID 11889123
XRCC4 - X-ray repair complementing defective repair in Chinese hamster cells 4 - HPRD 9430729
XRCC5 FLJ39089 | KARP-1 | KARP1 | KU80 | KUB2 | Ku86 | NFIV X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining) - HPRD 10207052|10446239
XRCC5 FLJ39089 | KARP-1 | KARP1 | KU80 | KUB2 | Ku86 | NFIV X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining) XRCC5 (Ku80) interacts with PRKDC (DNA-PKc). BIND 15758953
XRCC5 FLJ39089 | KARP-1 | KARP1 | KU80 | KUB2 | Ku86 | NFIV X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining) Affinity Capture-Western
in vitro
in vivo
Reconstituted Complex
BioGRID 9312071|10446239
|12393188
XRCC6 CTC75 | CTCBF | G22P1 | KU70 | ML8 | TLAA X-ray repair complementing defective repair in Chinese hamster cells 6 - HPRD 9312071|10446239
|11279128
XRCC6 CTC75 | CTCBF | G22P1 | KU70 | ML8 | TLAA X-ray repair complementing defective repair in Chinese hamster cells 6 Affinity Capture-Western
in vitro
in vivo
BioGRID 10064605|10446239


Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
KEGG NON HOMOLOGOUS END JOINING 14 8 All SZGR 2.0 genes in this pathway
KEGG CELL CYCLE 128 84 All SZGR 2.0 genes in this pathway
BIOCARTA G2 PATHWAY 24 20 All SZGR 2.0 genes in this pathway
BIOCARTA FAS PATHWAY 30 22 All SZGR 2.0 genes in this pathway
BIOCARTA HIVNEF PATHWAY 58 43 All SZGR 2.0 genes in this pathway
BIOCARTA TNFR1 PATHWAY 29 21 All SZGR 2.0 genes in this pathway
PID DNA PK PATHWAY 16 10 All SZGR 2.0 genes in this pathway
PID AR PATHWAY 61 46 All SZGR 2.0 genes in this pathway
PID PI3KCI AKT PATHWAY 35 30 All SZGR 2.0 genes in this pathway
PID BARD1 PATHWAY 29 19 All SZGR 2.0 genes in this pathway
REACTOME DOUBLE STRAND BREAK REPAIR 24 14 All SZGR 2.0 genes in this pathway
REACTOME DNA REPAIR 112 59 All SZGR 2.0 genes in this pathway
ONKEN UVEAL MELANOMA UP 783 507 All SZGR 2.0 genes in this pathway
SENGUPTA NASOPHARYNGEAL CARCINOMA UP 294 178 All SZGR 2.0 genes in this pathway
GAZDA DIAMOND BLACKFAN ANEMIA PROGENITOR DN 66 42 All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP 1382 904 All SZGR 2.0 genes in this pathway
DEURIG T CELL PROLYMPHOCYTIC LEUKEMIA UP 368 234 All SZGR 2.0 genes in this pathway
BORCZUK MALIGNANT MESOTHELIOMA UP 305 185 All SZGR 2.0 genes in this pathway
GAL LEUKEMIC STEM CELL UP 133 78 All SZGR 2.0 genes in this pathway
BASAKI YBX1 TARGETS UP 290 177 All SZGR 2.0 genes in this pathway
RHEIN ALL GLUCOCORTICOID THERAPY DN 362 238 All SZGR 2.0 genes in this pathway
KINSEY TARGETS OF EWSR1 FLII FUSION UP 1278 748 All SZGR 2.0 genes in this pathway
BIDUS METASTASIS UP 214 134 All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA DN 1375 806 All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA POORLY DIFFERENTIATED UP 633 376 All SZGR 2.0 genes in this pathway
ENK UV RESPONSE KERATINOCYTE DN 485 334 All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN DN 1781 1082 All SZGR 2.0 genes in this pathway
OUELLET OVARIAN CANCER INVASIVE VS LMP UP 117 85 All SZGR 2.0 genes in this pathway
MISSIAGLIA REGULATED BY METHYLATION DN 122 67 All SZGR 2.0 genes in this pathway
WAKASUGI HAVE ZNF143 BINDING SITES 58 33 All SZGR 2.0 genes in this pathway
FARMER BREAST CANCER CLUSTER 2 33 17 All SZGR 2.0 genes in this pathway
PATIL LIVER CANCER 747 453 All SZGR 2.0 genes in this pathway
MOHANKUMAR TLX1 TARGETS UP 414 287 All SZGR 2.0 genes in this pathway
GRUETZMANN PANCREATIC CANCER UP 358 245 All SZGR 2.0 genes in this pathway
PUJANA BREAST CANCER LIT INT NETWORK 101 73 All SZGR 2.0 genes in this pathway
PUJANA XPRSS INT NETWORK 168 103 All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK 1652 1023 All SZGR 2.0 genes in this pathway
PUJANA BRCA2 PCC NETWORK 423 265 All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK 1442 892 All SZGR 2.0 genes in this pathway
PUJANA CHEK2 PCC NETWORK 779 480 All SZGR 2.0 genes in this pathway
PUJANA BRCA CENTERED NETWORK 117 72 All SZGR 2.0 genes in this pathway
BENPORATH MYC MAX TARGETS 775 494 All SZGR 2.0 genes in this pathway
KAUFFMANN DNA REPAIR GENES 230 137 All SZGR 2.0 genes in this pathway
TARTE PLASMA CELL VS PLASMABLAST DN 309 206 All SZGR 2.0 genes in this pathway
FERNANDEZ BOUND BY MYC 182 116 All SZGR 2.0 genes in this pathway
REN BOUND BY E2F 61 40 All SZGR 2.0 genes in this pathway
ZHAN MULTIPLE MYELOMA SUBGROUPS 30 20 All SZGR 2.0 genes in this pathway
MOREAUX B LYMPHOCYTE MATURATION BY TACI DN 73 45 All SZGR 2.0 genes in this pathway
MOREAUX MULTIPLE MYELOMA BY TACI DN 172 107 All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS EARLY PROGENITOR 532 309 All SZGR 2.0 genes in this pathway
LEE AGING NEOCORTEX DN 80 49 All SZGR 2.0 genes in this pathway
MARSON BOUND BY E2F4 UNSTIMULATED 728 415 All SZGR 2.0 genes in this pathway
FUJII YBX1 TARGETS DN 202 132 All SZGR 2.0 genes in this pathway
MITSIADES RESPONSE TO APLIDIN DN 249 165 All SZGR 2.0 genes in this pathway
SMID BREAST CANCER RELAPSE IN BONE DN 315 197 All SZGR 2.0 genes in this pathway
BONOME OVARIAN CANCER SURVIVAL OPTIMAL DEBULKING 246 152 All SZGR 2.0 genes in this pathway
BOCHKIS FOXA2 TARGETS 425 261 All SZGR 2.0 genes in this pathway
GRADE COLON CANCER UP 871 505 All SZGR 2.0 genes in this pathway
GRADE COLON AND RECTAL CANCER UP 285 167 All SZGR 2.0 genes in this pathway
BLUM RESPONSE TO SALIRASIB DN 342 220 All SZGR 2.0 genes in this pathway
FIRESTEIN PROLIFERATION 175 125 All SZGR 2.0 genes in this pathway
SHEDDEN LUNG CANCER POOR SURVIVAL A6 456 285 All SZGR 2.0 genes in this pathway
DING LUNG CANCER BY MUTATION RATE 20 18 All SZGR 2.0 genes in this pathway
BOYAULT LIVER CANCER SUBCLASS G123 UP 45 21 All SZGR 2.0 genes in this pathway
FOURNIER ACINAR DEVELOPMENT LATE 2 277 172 All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA CLASSES UP 605 377 All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC 1103 714 All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS SENESCENT 572 352 All SZGR 2.0 genes in this pathway
WIERENGA PML INTERACTOME 42 23 All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 3 DN 918 550 All SZGR 2.0 genes in this pathway
ABRAMSON INTERACT WITH AIRE 45 33 All SZGR 2.0 genes in this pathway