SZGR2

Summary ?

GeneID	3736
Symbol	KCNA1
Synonyms	AEMK\|EA1\|HBK1\|HUK1\|KV1.1\|MBK1\|MK1\|RBK1
Description	potassium voltage-gated channel subfamily A member 1
Reference	MIM:176260\|HGNC:HGNC:6218\|Ensembl:ENSG00000111262\|HPRD:08885\|Vega:OTTHUMG00000044398
Gene type	protein-coding
Map location	12p13.32
Pascal p-value	0.005
Sherlock p-value	0.872
Fetal beta	-2.361
DMG	1 (# studies)
eGene	Myers' cis & trans
Support	EXCITABILITY

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
DMG:Nishioka_2013	Genome-wide DNA methylation analysis	The authors investigated the methylation profiles of DNA in peripheral blood cells from 18 patients with first-episode schizophrenia (FESZ) and from 15 normal controls.	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,schizophrenias	Click to show details
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 1

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg26590537	12	5020202	KCNA1		-0.02	0.54	DMG:Nishioka_2013

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs17048849	chr2	129626025	KCNA1	3736	0.09	trans
rs2197597	chr2	129638077	KCNA1	3736	0	trans
rs2897468	chr2	129711721	KCNA1	3736	0.04	trans
rs12463708	chr2	149073943	KCNA1	3736	0.12	trans
rs16829545	chr2	151977407	KCNA1	3736	2.552E-4	trans
rs12509866	chr4	173017639	KCNA1	3736	0.01	trans
rs6903775	chr6	9420439	KCNA1	3736	0.17	trans
rs1020772	chr9	76532511	KCNA1	3736	0.19	trans
rs6537895	chr9	138318523	KCNA1	3736	0.02	trans
rs10761452	chr10	61847680	KCNA1	3736	0.19	trans
rs1344796	chr12	76397104	KCNA1	3736	0	trans
rs7488439	chr12	105155814	KCNA1	3736	0.08	trans
rs17036489	chr12	105292283	KCNA1	3736	0.15	trans
rs11068670	chr12	118182168	KCNA1	3736	0.02	trans
rs10850897	chr12	118196074	KCNA1	3736	0.02	trans
rs17081039	chr13	66841328	KCNA1	3736	0.15	trans
rs1298114	chr14	32382282	KCNA1	3736	0.13	trans
rs16955618	chr15	29937543	KCNA1	3736	3.785E-4	trans
rs6032295	chr20	44178138	KCNA1	3736	3.34E-4	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
CHRM1	0.93	0.90
C2orf55	0.90	0.79
ADAMTS8	0.89	0.77
ARHGEF4	0.88	0.82
AC105206.1	0.87	0.86
KCNH3	0.87	0.82
DGKZ	0.87	0.83
CACNG3	0.87	0.90
PDE2A	0.86	0.87
GRIN1	0.86	0.79

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
HEBP2	-0.53	-0.64
BCL7C	-0.48	-0.52
C21orf57	-0.44	-0.41
C9orf46	-0.44	-0.40
RBMX2	-0.44	-0.41
EXOSC8	-0.44	-0.33
DYNLT1	-0.44	-0.45
FAM36A	-0.42	-0.34
RPL23A	-0.42	-0.39
UBE2L6	-0.42	-0.24

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005515	protein binding	IEA		-
GO:0005244	voltage-gated ion channel activity	IEA		-
GO:0005249	voltage-gated potassium channel activity	IEA		-
GO:0005251	delayed rectifier potassium channel activity	TAS		8845167
GO:0015079	potassium ion transmembrane transporter activity	TAS		8845167
GO:0030955	potassium ion binding	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007268	synaptic transmission	TAS	neuron, Synap, Neurotransmitter (GO term level: 6)	7842011
GO:0006811	ion transport	IEA		-
GO:0006813	potassium ion transport	IEA		-
GO:0006813	potassium ion transport	TAS		8845167
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0016020	membrane	IEA		-
GO:0016021	integral to membrane	IEA		-
GO:0008076	voltage-gated potassium channel complex	IEA		-
GO:0008076	voltage-gated potassium channel complex	TAS		8845167

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
REACTOME NEURONAL SYSTEM	279	221	All SZGR 2.0 genes in this pathway
REACTOME VOLTAGE GATED POTASSIUM CHANNELS	43	32	All SZGR 2.0 genes in this pathway
REACTOME POTASSIUM CHANNELS	98	68	All SZGR 2.0 genes in this pathway
ODONNELL TFRC TARGETS DN	139	76	All SZGR 2.0 genes in this pathway
SENESE HDAC1 TARGETS DN	260	143	All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK	1652	1023	All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK	1442	892	All SZGR 2.0 genes in this pathway
SCHLESINGER H3K27ME3 IN NORMAL AND METHYLATED IN CANCER	28	21	All SZGR 2.0 genes in this pathway
BENPORATH SUZ12 TARGETS	1038	678	All SZGR 2.0 genes in this pathway
BENPORATH EED TARGETS	1062	725	All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3	1118	744	All SZGR 2.0 genes in this pathway
BENPORATH PRC2 TARGETS	652	441	All SZGR 2.0 genes in this pathway
LEE AGING NEOCORTEX UP	89	59	All SZGR 2.0 genes in this pathway
MAHAJAN RESPONSE TO IL1A UP	81	52	All SZGR 2.0 genes in this pathway
LIN NPAS4 TARGETS DN	68	48	All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP	1305	895	All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME2 AND H3K27ME3	349	234	All SZGR 2.0 genes in this pathway
WONG ADULT TISSUE STEM MODULE	721	492	All SZGR 2.0 genes in this pathway
MIKKELSEN NPC HCP WITH H3K4ME3 AND H3K27ME3	210	148	All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION DN	1080	713	All SZGR 2.0 genes in this pathway
GOBERT CORE OLIGODENDROCYTE DIFFERENTIATION	40	28	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	4461	4467	1A	hsa-miR-10a	UACCCUGUAGAUCCGAAUUUGUG
miR-10	4461	4467	1A	hsa-miR-10b	UACCCUGUAGAACCGAAUUUGU
miR-101	1033	1040	1A,m8	hsa-miR-101	UACAGUACUGUGAUAACUGAAG
miR-124/506	1651	1657	m8	hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
miR-124/506	1651	1657	m8	hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
miR-125/351	1273	1280	1A,m8	hsa-miR-125b^brain	UCCCUGAGACCCUAACUUGUGA
miR-125/351	1273	1280	1A,m8	hsa-miR-125a^brain	UCCCUGAGACCCUUUAACCUGUG
miR-128	4588	4594	m8	hsa-miR-128a	UCACAGUGAACCGGUCUCUUUU
				hsa-miR-128b	UCACAGUGAACCGGUCUCUUUC
				hsa-miR-128a	UCACAGUGAACCGGUCUCUUUU
				hsa-miR-128b	UCACAGUGAACCGGUCUCUUUC
miR-133	1316	1322	1A	hsa-miR-133a	UUGGUCCCCUUCAACCAGCUGU
miR-133	1316	1322	1A	hsa-miR-133b	UUGGUCCCCUUCAACCAGCUA
miR-137	2897	2903	1A	hsa-miR-137	UAUUGCUUAAGAAUACGCGUAG
miR-144	1034	1040	1A	hsa-miR-144	UACAGUAUAGAUGAUGUACUAG
miR-153	5303	5310	1A,m8	hsa-miR-153	UUGCAUAGUCACAAAAGUGA
miR-155	1108	1114	m8	hsa-miR-155	UUAAUGCUAAUCGUGAUAGGGG
miR-18	596	603	1A,m8	hsa-miR-18a	UAAGGUGCAUCUAGUGCAGAUA
miR-18	596	603	1A,m8	hsa-miR-18b	UAAGGUGCAUCUAGUGCAGUUA
miR-182	4269	4275	1A	hsa-miR-182	UUUGGCAAUGGUAGAACUCACA
miR-186	1403	1409	m8	hsa-miR-186	CAAAGAAUUCUCCUUUUGGGCUU
miR-21	929	935	m8	hsa-miR-21^brain	UAGCUUAUCAGACUGAUGUUGA
miR-21	929	935	m8	hsa-miR-590	GAGCUUAUUCAUAAAAGUGCAG
miR-218	839	845	1A	hsa-miR-218^brain	UUGUGCUUGAUCUAACCAUGU
miR-221/222	3184	3190	1A	hsa-miR-221^brain	AGCUACAUUGUCUGCUGGGUUUC
miR-221/222	3184	3190	1A	hsa-miR-222^brain	AGCUACAUCUGGCUACUGGGUCUC
miR-25/32/92/363/367	1467	1474	1A,m8	hsa-miR-25^brain	CAUUGCACUUGUCUCGGUCUGA
				hsa-miR-32	UAUUGCACAUUACUAAGUUGC
				hsa-miR-92	UAUUGCACUUGUCCCGGCCUG
				hsa-miR-367	AAUUGCACUUUAGCAAUGGUGA
				hsa-miR-92b^SZ	UAUUGCACUCGUCCCGGCCUC
miR-27	1791	1797	m8	hsa-miR-27a^brain	UUCACAGUGGCUAAGUUCCGC
miR-27	1791	1797	m8	hsa-miR-27b^brain	UUCACAGUGGCUAAGUUCUGC
miR-323	3231	3237	m8	hsa-miR-323^brain	GCACAUUACACGGUCGACCUCU
miR-34/449	4267	4273	1A	hsa-miR-34a^brain	UGGCAGUGUCUUAGCUGGUUGUU
				hsa-miR-34c	AGGCAGUGUAGUUAGCUGAUUGC
				hsa-miR-449	UGGCAGUGUAUUGUUAGCUGGU
				hsa-miR-449b	AGGCAGUGUAUUGUUAGCUGGC
miR-342	1793	1799	1A	hsa-miR-342^brain	UCUCACACAGAAAUCGCACCCGUC
miR-34b	3277	3284	1A,m8	hsa-miR-34b	UAGGCAGUGUCAUUAGCUGAUUG
miR-363	4592	4598	1A	hsa-miR-363	AUUGCACGGUAUCCAUCUGUAA
miR-409-5p	4227	4234	1A,m8	hsa-miR-409-5p	AGGUUACCCGAGCAACUUUGCA
miR-448	5304	5310	1A	hsa-miR-448	UUGCAUAUGUAGGAUGUCCCAU
miR-452	4593	4599	m8	hsa-miR-452	UGUUUGCAGAGGAAACUGAGAC
miR-500	1465	1472	1A,m8	hsa-miR-500	AUGCACCUGGGCAAGGAUUCUG
miR-542-3p	5323	5329	m8	hsa-miR-542-3p	UGUGACAGAUUGAUAACUGAAA
miR-7	3448	3454	1A	hsa-miR-7^SZ	UGGAAGACUAGUGAUUUUGUUG
miR-9	3573	3580	1A,m8	hsa-miR-9^SZ	UCUUUGGUUAUCUAGCUGUAUGA
miR-93.hd/291-3p/294/295/302/372/373/520	3265	3271	1A	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	4269	4275	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: KCNA1