SZGR2

Summary ?

GeneID	1452
Symbol	CSNK1A1
Synonyms	CK1\|CK1a\|CKIa\|HEL-S-77p\|HLCDGP1\|PRO2975
Description	casein kinase 1 alpha 1
Reference	MIM:600505\|HGNC:HGNC:2451\|Ensembl:ENSG00000113712\|HPRD:02739\|Vega:OTTHUMG00000163463
Gene type	protein-coding
Map location	5q32
Pascal p-value	0.214
Sherlock p-value	0.843
Fetal beta	1.434
eGene	Myers' cis & trans
Support	G2Cdb.humanPSD G2Cdb.humanPSP

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
PMID:cooccur	High-throughput literature-search	Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
GSMA_I	Genome scan meta-analysis	Psr: 0.0032
GSMA_IIE	Genome scan meta-analysis (European-ancestry samples)	Psr: 0.01718
GSMA_IIA	Genome scan meta-analysis (All samples)	Psr: 0.00459
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenias	Click to show details
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.0752

Section I. Genetics and epigenetics annotation

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs4491879	chr3	189373908	CSNK1A1	1452		0.15		trans

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
SEC61A1	0.91	0.90
MTMR3	0.90	0.89
ZXDC	0.90	0.87
SEPN1	0.89	0.92
SUFU	0.89	0.87
PHF2	0.89	0.91
AMMECR1L	0.89	0.86
LIX1L	0.89	0.90
POFUT1	0.89	0.86
PATZ1	0.89	0.90

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
C5orf53	-0.71	-0.76
AF347015.27	-0.66	-0.76
S100B	-0.65	-0.74
ACOT13	-0.64	-0.68
MT-CO2	-0.64	-0.78
AF347015.31	-0.64	-0.76
HLA-F	-0.64	-0.66
AF347015.33	-0.63	-0.74
CA4	-0.63	-0.67
FXYD1	-0.63	-0.73

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0000166	nucleotide binding	IEA		-
GO:0005524	ATP binding	IEA		-
GO:0004674	protein serine/threonine kinase activity	IEA		-
GO:0016740	transferase activity	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0006468	protein amino acid phosphorylation	TAS		10777483
GO:0016055	Wnt receptor signaling pathway	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005829	cytosol	EXP		11955436 \|12000790 \|12820959 \|15327769 \|16753179
GO:0005737	cytoplasm	IEA		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
ACTA1	ACTA \| ASMA \| CFTD \| CFTD1 \| CFTDM \| MPFD \| NEM1 \| NEM2 \| NEM3	actin, alpha 1, skeletal muscle	Affinity Capture-MS	BioGRID	12062430
ADAP1	CENTA1 \| GCS1L \| p42IP4	ArfGAP with dual PH domains 1	-	HPRD,BioGRID	11278595
AP3B1	ADTB3 \| ADTB3A \| HPS \| HPS2 \| PE	adaptor-related protein complex 3, beta 1 subunit	-	HPRD	12062430
AXIN1	AXIN \| MGC52315	axin 1	-	HPRD,BioGRID	11884395
CHRM3	HM3	cholinergic receptor, muscarinic 3	-	HPRD,BioGRID	10777483
ERF	PE-2 \| PE2	Ets2 repressor factor	Co-purification	BioGRID	12062430
HMGB1	DKFZp686A04236 \| HMG1 \| HMG3 \| SBP-1	high-mobility group box 1	-	HPRD,BioGRID	12062430
HMGB2	HMG2	high-mobility group box 2	-	HPRD,BioGRID	12062430
KPNA2	IPOA1 \| QIP2 \| RCH1 \| SRP1alpha	karyopherin alpha 2 (RAG cohort 1, importin alpha 1)	-	HPRD,BioGRID	12062430
PPP1R14A	CPI-17 \| CPI17 \| PPP1INL	protein phosphatase 1, regulatory (inhibitor) subunit 14A	-	HPRD,BioGRID	12062430
PPP1R14A	CPI-17 \| CPI17 \| PPP1INL	protein phosphatase 1, regulatory (inhibitor) subunit 14A	-	HPRD	15003508
PPP2CA	PP2Ac \| PP2CA \| RP-C	protein phosphatase 2 (formerly 2A), catalytic subunit, alpha isoform	Affinity Capture-MS	BioGRID	12062430
PPP2R5A	B56A \| MGC131915 \| PR61A	protein phosphatase 2, regulatory subunit B', alpha isoform	-	HPRD	12062430
RCC1	CHC1 \| RCC1-I	regulator of chromosome condensation 1	-	HPRD,BioGRID	12062430
SYT9	FLJ45896	synaptotagmin IX	-	HPRD,BioGRID	12062430
TNFRSF1B	CD120b \| TBPII \| TNF-R-II \| TNF-R75 \| TNFBR \| TNFR1B \| TNFR2 \| TNFR80 \| p75 \| p75TNFR	tumor necrosis factor receptor superfamily, member 1B	-	HPRD,BioGRID	7559483

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG WNT SIGNALING PATHWAY	151	112	All SZGR 2.0 genes in this pathway
KEGG HEDGEHOG SIGNALING PATHWAY	56	42	All SZGR 2.0 genes in this pathway
BIOCARTA P35ALZHEIMERS PATHWAY	11	9	All SZGR 2.0 genes in this pathway
BIOCARTA P53HYPOXIA PATHWAY	23	21	All SZGR 2.0 genes in this pathway
BIOCARTA NFAT PATHWAY	56	45	All SZGR 2.0 genes in this pathway
BIOCARTA WNT PATHWAY	26	24	All SZGR 2.0 genes in this pathway
WNT SIGNALING	89	71	All SZGR 2.0 genes in this pathway
ST WNT BETA CATENIN PATHWAY	34	28	All SZGR 2.0 genes in this pathway
ST FAS SIGNALING PATHWAY	65	54	All SZGR 2.0 genes in this pathway
PID WNT NONCANONICAL PATHWAY	32	26	All SZGR 2.0 genes in this pathway
PID BETA CATENIN DEG PATHWAY	18	17	All SZGR 2.0 genes in this pathway
PID PS1 PATHWAY	46	39	All SZGR 2.0 genes in this pathway
PID NFAT 3PATHWAY	54	47	All SZGR 2.0 genes in this pathway
PID FOXO PATHWAY	49	43	All SZGR 2.0 genes in this pathway
PID HEDGEHOG GLI PATHWAY	48	35	All SZGR 2.0 genes in this pathway
PID P53 REGULATION PATHWAY	59	50	All SZGR 2.0 genes in this pathway
REACTOME SIGNALING BY WNT	65	41	All SZGR 2.0 genes in this pathway
REACTOME CTNNB1 PHOSPHORYLATION CASCADE	16	11	All SZGR 2.0 genes in this pathway
PARENT MTOR SIGNALING UP	567	375	All SZGR 2.0 genes in this pathway
TURASHVILI BREAST DUCTAL CARCINOMA VS DUCTAL NORMAL DN	198	110	All SZGR 2.0 genes in this pathway
TURASHVILI BREAST DUCTAL CARCINOMA VS LOBULAR NORMAL DN	69	43	All SZGR 2.0 genes in this pathway
THUM SYSTOLIC HEART FAILURE DN	244	147	All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP	1382	904	All SZGR 2.0 genes in this pathway
LAIHO COLORECTAL CANCER SERRATED UP	112	71	All SZGR 2.0 genes in this pathway
WANG LMO4 TARGETS UP	372	227	All SZGR 2.0 genes in this pathway
OSMAN BLADDER CANCER UP	404	246	All SZGR 2.0 genes in this pathway
GINESTIER BREAST CANCER ZNF217 AMPLIFIED UP	78	48	All SZGR 2.0 genes in this pathway
TIEN INTESTINE PROBIOTICS 24HR DN	214	133	All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA POORLY DIFFERENTIATED UP	633	376	All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA ANAPLASTIC UP	722	443	All SZGR 2.0 genes in this pathway
HAHTOLA MYCOSIS FUNGOIDES SKIN DN	27	20	All SZGR 2.0 genes in this pathway
ENK UV RESPONSE KERATINOCYTE DN	485	334	All SZGR 2.0 genes in this pathway
GAUSSMANN MLL AF4 FUSION TARGETS C UP	170	114	All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 DN	855	609	All SZGR 2.0 genes in this pathway
GRUETZMANN PANCREATIC CANCER UP	358	245	All SZGR 2.0 genes in this pathway
SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN DN	584	395	All SZGR 2.0 genes in this pathway
RICKMAN TUMOR DIFFERENTIATED WELL VS POORLY DN	382	224	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 6HR DN	514	330	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT AND CANCER BOX4 DN	32	22	All SZGR 2.0 genes in this pathway
COLIN PILOCYTIC ASTROCYTOMA VS GLIOBLASTOMA DN	28	21	All SZGR 2.0 genes in this pathway
STARK PREFRONTAL CORTEX 22Q11 DELETION UP	195	138	All SZGR 2.0 genes in this pathway
GALE APL WITH FLT3 MUTATED UP	56	35	All SZGR 2.0 genes in this pathway
KUMAR TARGETS OF MLL AF9 FUSION	405	264	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP	1691	1088	All SZGR 2.0 genes in this pathway
WELCSH BRCA1 TARGETS UP	198	132	All SZGR 2.0 genes in this pathway
CARDOSO RESPONSE TO GAMMA RADIATION AND 3AB	18	11	All SZGR 2.0 genes in this pathway
JIANG AGING CEREBRAL CORTEX DN	54	43	All SZGR 2.0 genes in this pathway
BILD SRC ONCOGENIC SIGNATURE	62	38	All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 6HR UP	953	554	All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 24HR UP	783	442	All SZGR 2.0 genes in this pathway
MARSON BOUND BY FOXP3 UNSTIMULATED	1229	713	All SZGR 2.0 genes in this pathway
KYNG DNA DAMAGE BY GAMMA AND UV RADIATION	88	65	All SZGR 2.0 genes in this pathway
KYNG DNA DAMAGE DN	195	135	All SZGR 2.0 genes in this pathway
FINETTI BREAST CANCERS KINOME GRAY	15	10	All SZGR 2.0 genes in this pathway
IWANAGA CARCINOGENESIS BY KRAS UP	170	107	All SZGR 2.0 genes in this pathway
BLUM RESPONSE TO SALIRASIB UP	245	159	All SZGR 2.0 genes in this pathway
VANTVEER BREAST CANCER BRCA1 DN	44	28	All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS UP	504	321	All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 2 DN	336	211	All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 3 DN	918	550	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-135	958	964	m8	hsa-miR-135a	UAUGGCUUUUUAUUCCUAUGUGA
miR-135	958	964	m8	hsa-miR-135b	UAUGGCUUUUCAUUCCUAUGUG
miR-141/200a	550	556	m8	hsa-miR-141	UAACACUGUCUGGUAAAGAUGG
miR-141/200a	550	556	m8	hsa-miR-200a	UAACACUGUCUGGUAACGAUGU
miR-155	662	668	1A	hsa-miR-155	UUAAUGCUAAUCGUGAUAGGGG
miR-186	1073	1079	m8	hsa-miR-186	CAAAGAAUUCUCCUUUUGGGCUU
miR-203.1	369	375	1A	hsa-miR-203	UGAAAUGUUUAGGACCACUAG
miR-30-5p	830	837	1A,m8	hsa-miR-30a-5p	UGUAAACAUCCUCGACUGGAAG
				hsa-miR-30c^brain	UGUAAACAUCCUACACUCUCAGC
				hsa-miR-30d^SZ	UGUAAACAUCCCCGACUGGAAG
				hsa-miR-30b^SZ	UGUAAACAUCCUACACUCAGCU
				hsa-miR-30e-5p	UGUAAACAUCCUUGACUGGA
miR-325	638	645	1A,m8	hsa-miR-325	CCUAGUAGGUGUCCAGUAAGUGU
miR-330	356	363	1A,m8	hsa-miR-330^brain	GCAAAGCACACGGCCUGCAGAGA
miR-409-3p	486	492	m8	hsa-miR-409-3p	CGAAUGUUGCUCGGUGAACCCCU
miR-493-5p	83	89	m8	hsa-miR-493-5p	UUGUACAUGGUAGGCUUUCAUU
miR-495	326	332	1A	hsa-miR-495^brain	AAACAAACAUGGUGCACUUCUUU
miR-9	539	546	1A,m8	hsa-miR-9^SZ	UCUUUGGUUAUCUAGCUGUAUGA

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: CSNK1A1