SZGR2

Summary ?

GeneID	57472
Symbol	CNOT6
Synonyms	CCR4\|Ccr4a
Description	CCR4-NOT transcription complex subunit 6
Reference	MIM:608951\|HGNC:HGNC:14099\|Ensembl:ENSG00000113300\|HPRD:12341\|Vega:OTTHUMG00000130935
Gene type	protein-coding
Map location	5q35.3
Pascal p-value	0.224
Sherlock p-value	0.182
Fetal beta	2.304
DMG	1 (# studies)
eGene	Myers' cis & trans

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
DMG:Wockner_2014	Genome-wide DNA methylation analysis	This dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24).	1
GSMA_IIA	Genome scan meta-analysis (All samples)	Psr: 0.0276

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg09544279	5	179921349	CNOT6	3.793E-4	-0.193	0.043	DMG:Wockner_2014

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs16829545	chr2	151977407	CNOT6	57472	6.923E-7	trans
rs7584986	chr2	184111432	CNOT6	57472	0.02	trans
rs3106445	chr3	165326464	CNOT6	57472	0.14	trans
rs1199915		0	CNOT6	57472	0.09	trans
rs520325	chr3	165361016	CNOT6	57472	0.05	trans
rs7787830	chr7	98797019	CNOT6	57472	0.07	trans
rs3118341	chr9	25185518	CNOT6	57472	0.16	trans
rs2393316	chr10	59333070	CNOT6	57472	0.1	trans
rs16955618	chr15	29937543	CNOT6	57472	7.932E-8	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
SACM1L	0.87	0.84
NDUFS1	0.86	0.82
SENP2	0.85	0.82
SLC25A40	0.85	0.83
C2orf30	0.85	0.81
CHM	0.84	0.84
FAM179B	0.84	0.81
FAR1	0.84	0.83
DDHD2	0.84	0.80
DPP8	0.83	0.81

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
IL32	-0.49	-0.43
CLEC3B	-0.47	-0.54
AF347015.21	-0.45	-0.29
C16orf74	-0.42	-0.39
AF347015.18	-0.42	-0.29
C1orf61	-0.41	-0.46
FAM159B	-0.40	-0.39
CSAG1	-0.40	-0.34
CLDN5	-0.39	-0.37
AC098691.2	-0.39	-0.31

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0000287	magnesium ion binding	IEA		-
GO:0003723	RNA binding	IEA		-
GO:0005515	protein binding	IEA		-
GO:0004527	exonuclease activity	IEA		-
GO:0016787	hydrolase activity	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0006355	regulation of transcription, DNA-dependent	IEA		-
GO:0006350	transcription	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005634	nucleus	IEA		-
GO:0005737	cytoplasm	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG RNA DEGRADATION	59	37	All SZGR 2.0 genes in this pathway
REACTOME DEADENYLATION OF MRNA	22	14	All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF MRNA	284	128	All SZGR 2.0 genes in this pathway
REACTOME DEADENYLATION DEPENDENT MRNA DECAY	48	29	All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF RNA	330	155	All SZGR 2.0 genes in this pathway
UDAYAKUMAR MED1 TARGETS UP	135	82	All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN DN	1781	1082	All SZGR 2.0 genes in this pathway
GRAESSMANN RESPONSE TO MC AND DOXORUBICIN DN	770	415	All SZGR 2.0 genes in this pathway
DOUGLAS BMI1 TARGETS UP	566	371	All SZGR 2.0 genes in this pathway
MARSON BOUND BY E2F4 UNSTIMULATED	728	415	All SZGR 2.0 genes in this pathway
ZHANG BREAST CANCER PROGENITORS UP	425	253	All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA CLASSES UP	605	377	All SZGR 2.0 genes in this pathway
PANGAS TUMOR SUPPRESSION BY SMAD1 AND SMAD5 DN	157	106	All SZGR 2.0 genes in this pathway
IKEDA MIR30 TARGETS UP	116	87	All SZGR 2.0 genes in this pathway
FORTSCHEGGER PHF8 TARGETS UP	279	155	All SZGR 2.0 genes in this pathway
FORTSCHEGGER PHF8 TARGETS DN	784	464	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-10	3699	3705	m8	hsa-miR-10a	UACCCUGUAGAUCCGAAUUUGUG
miR-10	3699	3705	m8	hsa-miR-10b	UACCCUGUAGAACCGAAUUUGU
miR-128	933	939	m8	hsa-miR-128a	UCACAGUGAACCGGUCUCUUUU
				hsa-miR-128b	UCACAGUGAACCGGUCUCUUUC
				hsa-miR-128a	UCACAGUGAACCGGUCUCUUUU
				hsa-miR-128b	UCACAGUGAACCGGUCUCUUUC
miR-130/301	616	622	m8	hsa-miR-130a^brain	CAGUGCAAUGUUAAAAGGGCAU
				hsa-miR-301	CAGUGCAAUAGUAUUGUCAAAGC
				hsa-miR-130b^brain	CAGUGCAAUGAUGAAAGGGCAU
				hsa-miR-454-3p	UAGUGCAAUAUUGCUUAUAGGGUUU
				hsa-miR-130a^brain	CAGUGCAAUGUUAAAAGGGCAU
				hsa-miR-301	CAGUGCAAUAGUAUUGUCAAAGC
				hsa-miR-130b^brain	CAGUGCAAUGAUGAAAGGGCAU
				hsa-miR-454-3p	UAGUGCAAUAUUGCUUAUAGGGUUU
miR-148/152	3482	3488	m8	hsa-miR-148a	UCAGUGCACUACAGAACUUUGU
				hsa-miR-152^brain	UCAGUGCAUGACAGAACUUGGG
				hsa-miR-148b	UCAGUGCAUCACAGAACUUUGU
miR-17-5p/20/93.mr/106/519.d	3043	3049	m8	hsa-miR-17-5p	CAAAGUGCUUACAGUGCAGGUAGU
				hsa-miR-20a^brain	UAAAGUGCUUAUAGUGCAGGUAG
				hsa-miR-106a	AAAAGUGCUUACAGUGCAGGUAGC
				hsa-miR-106b^SZ	UAAAGUGCUGACAGUGCAGAU
				hsa-miR-20b^SZ	CAAAGUGCUCAUAGUGCAGGUAG
				hsa-miR-519d	CAAAGUGCCUCCCUUUAGAGUGU
miR-182	3991	3998	1A,m8	hsa-miR-182	UUUGGCAAUGGUAGAACUCACA
miR-19	615	621	m8	hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
miR-19	615	621	m8	hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
miR-193	356	363	1A,m8	hsa-miR-193a	AACUGGCCUACAAAGUCCCAG
miR-193	356	363	1A,m8	hsa-miR-193b	AACUGGCCCUCAAAGUCCCGCUUU
miR-199	3484	3490	1A	hsa-miR-199a	CCCAGUGUUCAGACUACCUGUUC
miR-199	3484	3490	1A	hsa-miR-199b	CCCAGUGUUUAGACUAUCUGUUC
miR-200bc/429	3363	3369	m8	hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
miR-21	770	776	m8	hsa-miR-21^brain	UAGCUUAUCAGACUGAUGUUGA
miR-21	770	776	m8	hsa-miR-590	GAGCUUAUUCAUAAAAGUGCAG
miR-24	176	182	m8	hsa-miR-24^SZ	UGGCUCAGUUCAGCAGGAACAG
miR-29	155	161	1A	hsa-miR-29a^SZ	UAGCACCAUCUGAAAUCGGUU
				hsa-miR-29b^SZ	UAGCACCAUUUGAAAUCAGUGUU
				hsa-miR-29c^SZ	UAGCACCAUUUGAAAUCGGU
miR-30-5p	3499	3505	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-320	2236	2242	1A	hsa-miR-320	AAAAGCUGGGUUGAGAGGGCGAA
miR-329	213	219	m8	hsa-miR-329^brain	AACACACCUGGUUAACCUCUUU
miR-339	203	210	1A,m8	hsa-miR-339	UCCCUGUCCUCCAGGAGCUCA
miR-34/449	965	971	m8	hsa-miR-34a^brain	UGGCAGUGUCUUAGCUGGUUGUU
				hsa-miR-34c	AGGCAGUGUAGUUAGCUGAUUGC
				hsa-miR-449	UGGCAGUGUAUUGUUAGCUGGU
				hsa-miR-449b	AGGCAGUGUAUUGUUAGCUGGC
miR-342	1032	1038	1A	hsa-miR-342^brain	UCUCACACAGAAAUCGCACCCGUC
miR-34b	966	972	m8	hsa-miR-34b	UAGGCAGUGUCAUUAGCUGAUUG
miR-377	1961	1967	1A	hsa-miR-377	AUCACACAAAGGCAACUUUUGU
miR-381	453	459	1A	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-382	727	733	1A	hsa-miR-382^brain	GAAGUUGUUCGUGGUGGAUUCG
miR-410	3693	3699	1A	hsa-miR-410	AAUAUAACACAGAUGGCCUGU
miR-433-3p	2017	2023	m8	hsa-miR-433^brain	AUCAUGAUGGGCUCCUCGGUGU
miR-485-3p	143	149	1A	hsa-miR-485-3p	GUCAUACACGGCUCUCCUCUCU
miR-493-5p	827	833	m8	hsa-miR-493-5p	UUGUACAUGGUAGGCUUUCAUU
miR-494	3762	3768	1A	hsa-miR-494^brain	UGAAACAUACACGGGAAACCUCUU
miR-494	3762	3768	1A	hsa-miR-494^brain	UGAAACAUACACGGGAAACCUCUU
miR-495	2164	2170	1A	hsa-miR-495^brain	AAACAAACAUGGUGCACUUCUUU
miR-504	3700	3706	m8	hsa-miR-504	AGACCCUGGUCUGCACUCUAU
miR-7	382	388	1A	hsa-miR-7^SZ	UGGAAGACUAGUGAUUUUGUUG
miR-93.hd/291-3p/294/295/302/372/373/520	2145	2152	1A,m8	hsa-miR-93^brain	AAAGUGCUGUUCGUGCAGGUAG
				hsa-miR-302a	UAAGUGCUUCCAUGUUUUGGUGA
				hsa-miR-302b	UAAGUGCUUCCAUGUUUUAGUAG
				hsa-miR-302c	UAAGUGCUUCCAUGUUUCAGUGG
				hsa-miR-302d	UAAGUGCUUCCAUGUUUGAGUGU
				hsa-miR-372	AAAGUGCUGCGACAUUUGAGCGU
				hsa-miR-373	GAAGUGCUUCGAUUUUGGGGUGU
				hsa-miR-520e	AAAGUGCUUCCUUUUUGAGGG
				hsa-miR-520a	AAAGUGCUUCCCUUUGGACUGU
				hsa-miR-520b	AAAGUGCUUCCUUUUAGAGGG
				hsa-miR-520c	AAAGUGCUUCCUUUUAGAGGGUU
				hsa-miR-520d	AAAGUGCUUCUCUUUGGUGGGUU
				hsa-miR-93^brain	AAAGUGCUGUUCGUGCAGGUAG
				hsa-miR-302a	UAAGUGCUUCCAUGUUUUGGUGA
				hsa-miR-302b	UAAGUGCUUCCAUGUUUUAGUAG
				hsa-miR-302c	UAAGUGCUUCCAUGUUUCAGUGG
				hsa-miR-302d	UAAGUGCUUCCAUGUUUGAGUGU
				hsa-miR-372	AAAGUGCUGCGACAUUUGAGCGU
				hsa-miR-373	GAAGUGCUUCGAUUUUGGGGUGU
				hsa-miR-520e	AAAGUGCUUCCUUUUUGAGGG
				hsa-miR-520a	AAAGUGCUUCCCUUUGGACUGU
				hsa-miR-520b	AAAGUGCUUCCUUUUAGAGGG
				hsa-miR-520c	AAAGUGCUUCCUUUUAGAGGGUU
				hsa-miR-520d	AAAGUGCUUCUCUUUGGUGGGUU
miR-96	3992	3998	1A	hsa-miR-96^brain	UUUGGCACUAGCACAUUUUUGC

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: CNOT6