SZGR2

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	Co-occurance with Schizophrenia 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)

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	IPI		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 regulatory subunit associated protein 1	-	HPRD,BioGRID	11882646
CDK5RAP2	C48 \| Cep215 \| DKFZp686B1070 \| DKFZp686D1070 \| KIAA1633 \| MCPH3	CDK5 regulatory subunit associated protein 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
miRNA family	UTR start	UTR end	Match method	miRNA ID	miRNA seq
miR-142-5p	158	164	m8	hsa-miR-142-5p	CAUAAAGUAGAAAGCACUAC

SZ: miRNAs which differentially expressed in brain cortex of schizophrenia patients comparing with control samples using microarray. Click here to see the list of SZ related miRNAs.
Brain: miRNAs which are expressed in brain based on miRNA microarray expression studies. Click here to see the list of brain related miRNAs.

Gene Page: CDK5