Gene Page:CDK5

Summary?
GeneID 1020
Symbol CDK5
Synonyms LIS7|PSSALRE
Description cyclin-dependent kinase 5
Reference MIM:123831|HGNC:HGNC:1774|HPRD:00449|
Gene type protein-coding
Map location 7q36
Pascal p-value 7.015E-4
Sherlock p-value 0.188
Fetal beta -0.927
DMG 1 (# studies)
Support G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS
G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL
G2Cdb.human_BAYES-COLLINS-MOUSE-PSD-CONSENSUS
G2Cdb.humanPSD
G2Cdb.humanPSP
CompositeSet
Potential synaptic genes

Gene in Data Sources
Gene set name Method of gene set Description Info
CV:PGCnp Genome-wide Association Study GWAS
DMG:Jaffe_2016 Genome-wide DNA methylation analysis This dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 1
PMID:cooccur High-throughput literature-search Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
Literature High-throughput literature-search 与精神分裂症Co-occurance keywords: schizophrenia,schizophrenic,schizophrenias Click to show details
GO_Annotation Mapping neuro-related keywords to Gene Ontology annotations Hits with neuro-related keywords: 14
Network Shortest path distance of core genes in the Human protein-protein interaction network Contribution to shortest path in PPI network: 0.152

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

Probe Chromosome Position Nearest gene P (dis) Beta (dis) FDR (dis) Study
cg11368578 7 150754936 CDK5 4.21E-10 -0.016 7.8E-7 DMG:Jaffe_2016


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
C1R 0.66 0.76
PTH1R 0.64 0.68
PLCD3 0.62 0.72
ANKRD9 0.59 0.64
SDSL 0.58 0.63
GNPTG 0.57 0.66
SERTAD1 0.57 0.66
OCEL1 0.57 0.60
ARID5A 0.56 0.66
LDHD 0.56 0.61
Top 10 negatively co-expressed genes
Gene Pearson's Correlation Spearman's Correlation
ZNF551 -0.48 -0.51
AC004017.1 -0.48 -0.52
ZNF435 -0.48 -0.55
ZNF124 -0.47 -0.54
MLLT3 -0.47 -0.49
ZNF302 -0.47 -0.54
KIAA1949 -0.47 -0.36
ZNF766 -0.47 -0.53
ZNF34 -0.47 -0.51
PPAPDC1B -0.47 -0.50

Section III. Gene Ontology annotation

Molecular function GO term Evidence Neuro keywords PubMed ID
GO:0004693 cyclin-dependent protein kinase activity TAS neuron (GO term level: 8) 8090221
GO:0050321 tau-protein kinase activity ISS Brain (GO term level: 7) -
GO:0000166 nucleotide binding IEA -
GO:0005176 ErbB-2 class receptor binding ISS -
GO:0005515 protein binding 新闻学会 12223541
GO:0005515 protein binding ISS -
GO:0005524 ATP binding IEA -
GO:0016740 transferase activity IEA -
GO:0030549 acetylcholine receptor activator activity ISS -
GO:0043125 ErbB-3 class receptor binding ISS -
Biological process GO term Evidence Neuro keywords PubMed ID
GO:0007409 axonogenesis IEA neuron, axon, neurite (GO term level: 12) -
GO:0008045 motor axon guidance IEA neuron, axon (GO term level: 14) -
GO:0030182 neuron differentiation ISS neuron (GO term level: 8) -
GO:0060078 regulation of postsynaptic membrane potential IEA neuron, Synap, Neurotransmitter (GO term level: 9) -
GO:0014044 Schwann cell development IEA neuron, axon, Glial (GO term level: 10) -
GO:0031175 neurite development ISS neuron, axon, neurite, dendrite (GO term level: 10) -
GO:0043525 positive regulation of neuron apoptosis ISS neuron (GO term level: 9) -
GO:0007160 cell-matrix adhesion IEA -
GO:0006468 protein amino acid phosphorylation IEA -
GO:0007049 cell cycle IEA -
GO:0008283 cell proliferation TAS 8090221
GO:0009790 embryonic development ISS -
GO:0051301 cell division IEA -
GO:0030334 regulation of cell migration IEA -
GO:0043113 receptor clustering IEA -
GO:0045860 positive regulation of protein kinase activity IEA -
Cellular component GO term Evidence Neuro keywords PubMed ID
GO:0043025 cell soma ISS axon, dendrite (GO term level: 4) -
GO:0030175 filopodium IEA axon (GO term level: 5) -
GO:0031594 neuromuscular junction ISS neuron, axon, Synap, Neurotransmitter (GO term level: 3) -
GO:0030426 growth cone ISS axon, dendrite (GO term level: 5) -
GO:0030425 dendrite ISS neuron, axon, dendrite (GO term level: 6) -
GO:0030424 axon ISS neuron, axon, Neurotransmitter (GO term level: 6) -
GO:0005829 cytosol IEA -
GO:0005634 nucleus ISS -
GO:0005737 cytoplasm ISS -
GO:0016020 membrane ISS -
GO:0030027 lamellipodium IEA -

Section IV. Protein-protein interaction annotation

Interactors Aliases B Official full name B Experimental Source PubMed ID
BRCA1 BRCAI | BRCC1 | IRIS | PSCP | RNF53 breast cancer 1, early onset Reconstituted Complex BioGRID 9244350
CABLES1 CABLES | FLJ35924 | HsT2563 | IK3-1 Cdk5 and Abl enzyme substrate 1 - HPRD 10896159|11733001
|11955625
CABLES2 C20orf150 | dJ908M14.2 | ik3-2 Cdk5 and Abl enzyme substrate 2 - HPRD,BioGRID 11955625
CCND2 KIAK0002 | MGC102758 cyclin D2 - HPRD,BioGRID 9422379
CCNG1 CCNG cyclin G1 - HPRD 9013862
CDK5 PSSALRE cyclin-dependent kinase 5 - HPRD,BioGRID 11583627
CDK5R1 CDK5P35 | CDK5R | MGC33831 | NCK5A | p23 | p25 | p35 | p35nck5a cyclin-dependent kinase 5, regulatory subunit 1 (p35) p35 interacts with Cdk5. This interaction was modeled on a demonstrated interaction between bovine p35 and human Cdk5. BIND 9038181
CDK5R1 CDK5P35 | CDK5R | MGC33831 | NCK5A | p23 | p25 | p35 | p35nck5a cyclin-dependent kinase 5, regulatory subunit 1 (p35) - HPRD,BioGRID 11583627
CDK5R1 CDK5P35 | CDK5R | MGC33831 | NCK5A | p23 | p25 | p35 | p35nck5a cyclin-dependent kinase 5, regulatory subunit 1 (p35) Cdk5 interacts with p35. BIND 8090221
CDK5R2 NCK5AI | P39 | p39nck5ai cyclin-dependent kinase 5, regulatory subunit 2 (p39) - HPRD,BioGRID 10683146
CDK5RAP1 C20orf34 | C42 | CDK5RAP1.3 | CDK5RAP1.4 | CGI-05 | HSPC167 CDK5调节亚基相关的蛋白质n 1 - HPRD,BioGRID 11882646
CDK5RAP2 C48 | Cep215 | DKFZp686B1070 | DKFZp686D1070 | KIAA1633 | MCPH3 CDK5调节亚基相关的蛋白质n 2 Reconstituted Complex BioGRID 10915792
CTNNB1 CTNNB | DKFZp686D02253 | FLJ25606 | FLJ37923 catenin (cadherin-associated protein), beta 1, 88kDa - HPRD 11168528
FSD1 GLFND | MGC3213 | MIR1 fibronectin type III and SPRY domain containing 1 - HPRD 12154070
GAK FLJ16629 | FLJ40395 | MGC99654 cyclin G associated kinase - HPRD,BioGRID 9013862
LMTK2 AATYK2 | BREK | KIAA1079 | KPI-2 | KPI2 | LMR2 | cprk lemur tyrosine kinase 2 Reconstituted Complex
Two-hybrid		 BioGRID 12832520
NDEL1 DKFZp451M0318 | EOPA | MITAP1 | NUDEL nudE nuclear distribution gene E homolog (A. nidulans)-like 1 Biochemical Activity
Co-localization		 BioGRID 11163260
NES FLJ21841 | Nbla00170 nestin - HPRD,BioGRID 12832492
PAK1 MGC130000 | MGC130001 | PAKalpha p21 protein (Cdc42/Rac)-activated kinase 1 Affinity Capture-Western
Biochemical Activity		 BioGRID 11604394
PCNA MGC8367 proliferating cell nuclear antigen - HPRD 7949095
PCTK1 FLJ16665 | PCTAIRE | PCTAIRE1 | PCTGAIRE PCTAIRE protein kinase 1 Biochemical Activity BioGRID 12084709
STX1A HPC-1 | STX1 | p35-1 syntaxin 1A (brain) - HPRD,BioGRID 9478941
STXBP1 EIEE4 | MUNC18-1 | UNC18 | hUNC18 | rbSec1 syntaxin binding protein 1 - HPRD,BioGRID 12963086


Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
KEGG AXON GUIDANCE 129 103 All SZGR 2.0 genes in this pathway
KEGG ALZHEIMERS DISEASE 169 110 All SZGR 2.0 genes in this pathway
BIOCARTA BIOPEPTIDES PATHWAY 45 35 All SZGR 2.0 genes in this pathway
BIOCARTA P35ALZHEIMERS PATHWAY 11 9 All SZGR 2.0 genes in this pathway
BIOCARTA CDK5 PATHWAY 11 11 All SZGR 2.0 genes in this pathway
BIOCARTA RAC1 PATHWAY 23 16 All SZGR 2.0 genes in this pathway
BIOCARTA CK1 PATHWAY 17 17 All SZGR 2.0 genes in this pathway
PID REELIN PATHWAY 29 29 All SZGR 2.0 genes in this pathway
PID REG GR PATHWAY 82 60 All SZGR 2.0 genes in this pathway
PID LIS1 PATHWAY 28 22 All SZGR 2.0 genes in this pathway
PID EPHA FWDPATHWAY 34 29 All SZGR 2.0 genes in this pathway
PID MAPK TRK PATHWAY 34 31 All SZGR 2.0 genes in this pathway
REACTOME DEVELOPMENTAL BIOLOGY 396 292 All SZGR 2.0 genes in this pathway
REACTOME SIGNALING BY GPCR 920 449 All SZGR 2.0 genes in this pathway
REACTOME OPIOID SIGNALLING 78 56 All SZGR 2.0 genes in this pathway
REACTOME DARPP 32 EVENTS 25 20 All SZGR 2.0 genes in this pathway
REACTOME AXON GUIDANCE 251 188 All SZGR 2.0 genes in this pathway
REACTOME CRMPS IN SEMA3A SIGNALING 14 14 All SZGR 2.0 genes in this pathway
REACTOME SEMAPHORIN INTERACTIONS 68 53 All SZGR 2.0 genes in this pathway
REACTOME FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION 132 101 All SZGR 2.0 genes in this pathway
REACTOME HEMOSTASIS 466 331 All SZGR 2.0 genes in this pathway
KOKKINAKIS METHIONINE DEPRIVATION 48HR DN 64 39 All SZGR 2.0 genes in this pathway
KOKKINAKIS METHIONINE DEPRIVATION 96HR DN 75 50 All SZGR 2.0 genes in this pathway
ENK UV RESPONSE KERATINOCYTE UP 530 342 All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY SERUM DEPRIVATION UP 552 347 All SZGR 2.0 genes in this pathway
SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN UP 479 299 All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS DN 1024 594 All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS DN 637 377 All SZGR 2.0 genes in this pathway
LOPEZ MBD TARGETS 957 597 All SZGR 2.0 genes in this pathway
LOCKWOOD AMPLIFIED IN LUNG CANCER 214 139 All SZGR 2.0 genes in this pathway
STARK PREFRONTAL CORTEX 22Q11 DELETION DN 517 309 All SZGR 2.0 genes in this pathway
ABRAHAM ALPC VS MULTIPLE MYELOMA DN 19 14 All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS LATE PROGENITOR 544 307 All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN 1237 837 All SZGR 2.0 genes in this pathway
MURAKAMI UV RESPONSE 6HR DN 21 13 All SZGR 2.0 genes in this pathway
SESTO RESPONSE TO UV C4 20 14 All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER UP 973 570 All SZGR 2.0 genes in this pathway
ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE UP 863 514 All SZGR 2.0 genes in this pathway
BOCHKIS FOXA2 TARGETS 425 261 All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 1HR DN 222 147 All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 4HR DN 254 158 All SZGR 2.0 genes in this pathway
MARTENS BOUND BY PML RARA FUSION 456 287 All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS OLIGODENDROCYTE NUMBER CORR UP 756 494 All SZGR 2.0 genes in this pathway
KIM BIPOLAR DISORDER OLIGODENDROCYTE DENSITY CORR UP 682 440 All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS CALB1 CORR UP 548 370 All SZGR 2.0 genes in this pathway
KOINUMA TARGETS OF SMAD2 OR SMAD3 824 528 All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION DN 1080 713 All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA family Target position miRNA ID miRNA seq
UTR start UTR end Match method
miR-142-5p 158 164 m8 hsa-miR-142-5p CAUAAAGUAGAAAGCACUAC