SZGR2

Summary ?

GeneID	266743
Symbol	NPAS4
Synonyms	Le-PAS\|NXF\|PASD10\|bHLHe79
Description	neuronal PAS domain protein 4
Reference	MIM:608554\|HGNC:HGNC:18983\|Ensembl:ENSG00000174576\|HPRD:12260\|Vega:OTTHUMG00000167045
Gene type	protein-coding
Map location	11q13
Pascal p-value	0.009
Fetal beta	-1.205
DMG	1 (# studies)
eGene	Cerebellar Hemisphere Myers' cis & trans

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

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg24057637	11	66176608	NPAS4	2.8E-8	-0.014	8.75E-6	DMG:Jaffe_2016

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs17126801	chr1	65098162	NPAS4	266743	0.01	trans
rs2566762	chr1	68582456	NPAS4	266743	0.03	trans
rs17100231	chr1	77761339	NPAS4	266743	0.01	trans
rs17100274	chr1	77774412	NPAS4	266743	7.223E-6	trans
rs16837984	chr1	157042626	NPAS4	266743	0.19	trans
rs16838012	chr1	157048974	NPAS4	266743	0.19	trans
rs16838014		0	NPAS4	266743	0.19	trans
rs6666937	chr1	170286842	NPAS4	266743	5.753E-10	trans
rs16843112	chr1	198420657	NPAS4	266743	9.211E-4	trans
rs6673109	chr1	207253132	NPAS4	266743	0.19	trans
rs17044576	chr1	207634669	NPAS4	266743	0.05	trans
rs1796829	chr1	239661818	NPAS4	266743	0.19	trans
rs12034521	chr1	239717679	NPAS4	266743	0.1	trans
snp_a-1990354		0	NPAS4	266743	0.02	trans
rs12465555	chr2	44118188	NPAS4	266743	0.1	trans
rs17038084	chr2	85192280	NPAS4	266743	0.09	trans
rs17024035	chr2	100968559	NPAS4	266743	4.091E-5	trans
rs7574684	chr2	100992911	NPAS4	266743	4.091E-5	trans
rs17024129	chr2	100995144	NPAS4	266743	4.091E-5	trans
rs17024136	chr2	100995382	NPAS4	266743	0	trans
rs7585898	chr2	100998292	NPAS4	266743	4.091E-5	trans
rs6716367	chr2	101000013	NPAS4	266743	0	trans
rs1370627	chr2	101009384	NPAS4	266743	4.091E-5	trans
rs4149509	chr2	101023698	NPAS4	266743	0	trans
rs6707117	chr2	136855504	NPAS4	266743	3.758E-4	trans
rs16838911	chr2	156087569	NPAS4	266743	2.256E-4	trans
rs9807949	chr2	182655005	NPAS4	266743	0.17	trans
rs7608942	chr2	182820100	NPAS4	266743	2.416E-6	trans
rs17199614	chr2	232457856	NPAS4	266743	0.01	trans
rs17684934	chr3	4443547	NPAS4	266743	0.16	trans
rs17040633	chr3	4446836	NPAS4	266743	0.16	trans
rs17756483	chr3	4451309	NPAS4	266743	0.16	trans
rs17685441	chr3	4465165	NPAS4	266743	0.16	trans
rs6772815	chr3	5164768	NPAS4	266743	0.06	trans
rs997245	chr3	61844600	NPAS4	266743	7.283E-6	trans
rs6807632	chr3	111395567	NPAS4	266743	0	trans
rs4469113	chr4	41461062	NPAS4	266743	0.12	trans
rs6881821	chr5	8578465	NPAS4	266743	0.15	trans
rs2115110	chr5	38193428	NPAS4	266743	0.04	trans
rs10040715	chr5	57594207	NPAS4	266743	2.793E-5	trans
snp_a-4217300		0	NPAS4	266743	0.03	trans
rs17134275	chr5	100634998	NPAS4	266743	0.18	trans
rs10063272	chr5	103540974	NPAS4	266743	0.12	trans
rs2963232	chr5	103713882	NPAS4	266743	0.01	trans
rs2900115	chr5	117414349	NPAS4	266743	0.07	trans
rs2141482	chr5	136760477	NPAS4	266743	1.019E-5	trans
rs2189803	chr5	137684661	NPAS4	266743	0	trans
rs17209139	chr5	142552525	NPAS4	266743	0.01	trans
rs259913	chr5	169370782	NPAS4	266743	0.04	trans
rs2116811	chr5	171820051	NPAS4	266743	0.19	trans
rs2239516	chr6	30578047	NPAS4	266743	0.05	trans
rs6904236	chr6	30596134	NPAS4	266743	0.04	trans
rs16884095	chr6	53470796	NPAS4	266743	0.01	trans
rs2030024	chr6	131014624	NPAS4	266743	0	trans
rs10485094	chr6	131071433	NPAS4	266743	4.244E-4	trans
rs17059517	chr6	131076254	NPAS4	266743	0	trans
rs9402280	chr6	131102770	NPAS4	266743	0.01	trans
rs12164028	chr6	136929934	NPAS4	266743	0	trans
rs10872699	chr6	153544252	NPAS4	266743	0.02	trans
rs1321606	chr6	153545278	NPAS4	266743	0.19	trans
rs10945911	chr6	164047509	NPAS4	266743	7.821E-4	trans
rs320082	chr7	29105404	NPAS4	266743	0.03	trans
rs317720	chr7	29110633	NPAS4	266743	0.17	trans
rs317714	chr7	29115553	NPAS4	266743	0.01	trans
rs317724	chr7	29120565	NPAS4	266743	0.17	trans
rs12701006	chr7	30147298	NPAS4	266743	0.04	trans
rs1419793	chr7	34697630	NPAS4	266743	9.733E-7	trans
rs17141666	chr7	69928490	NPAS4	266743	0.18	trans
rs10487383	chr7	117671737	NPAS4	266743	0.17	trans
rs3993439	chr7	128679933	NPAS4	266743	0.2	trans
rs1562835	chr7	131832157	NPAS4	266743	0.06	trans
rs7829733	chr8	9691720	NPAS4	266743	0.08	trans
rs4921933	chr8	18375289	NPAS4	266743	0.03	trans
rs12676224	chr8	18375316	NPAS4	266743	0.02	trans
rs10102886	chr8	51805574	NPAS4	266743	5.959E-4	trans
rs1457044	chr8	59257567	NPAS4	266743	0.03	trans
rs1733950	chr8	90062516	NPAS4	266743	7.803E-5	trans
rs1240028	chr8	90093357	NPAS4	266743	0.06	trans
rs1240087	chr8	90113945	NPAS4	266743	0.17	trans
rs318307	chr8	90185459	NPAS4	266743	0.07	trans
rs3136426	chr8	95447406	NPAS4	266743	0.09	trans
rs4976941	chr8	142744439	NPAS4	266743	0.05	trans
rs9298651	chr9	10076275	NPAS4	266743	0	trans
rs16931013	chr9	10076859	NPAS4	266743	0	trans
rs16931018	chr9	10077048	NPAS4	266743	0	trans
rs1335159	chr9	31147839	NPAS4	266743	0.02	trans
rs1109460	chr9	79410224	NPAS4	266743	0	trans
rs11791891	chr9	87512411	NPAS4	266743	0	trans
rs2165893	chr9	87531423	NPAS4	266743	4.568E-4	trans
rs17087869	chr9	87535284	NPAS4	266743	0	trans
rs763623	chr9	87539663	NPAS4	266743	2.924E-5	trans
rs3780642	chr9	87553144	NPAS4	266743	1.111E-6	trans
rs3780645	chr9	87559793	NPAS4	266743	0.18	trans
rs10981864	chr9	116416735	NPAS4	266743	0.04	trans
rs2417062	chr9	130715921	NPAS4	266743	0.02	trans
rs12005879	chr9	133737648	NPAS4	266743	0.2	trans
rs3104871	chr10	57878502	NPAS4	266743	0.1	trans
rs3913912	chr10	83014160	NPAS4	266743	0.03	trans
rs7090183	chr10	83017859	NPAS4	266743	0.03	trans
rs7086676	chr10	83018033	NPAS4	266743	0.03	trans
rs769442	chr11	64888954	NPAS4	266743	0.01	trans
rs2239031	chr12	2336168	NPAS4	266743	0.01	trans
rs2109556	chr12	3887300	NPAS4	266743	0.06	trans
rs8490	chr12	51453904	NPAS4	266743	0.02	trans
rs17113079	chr12	74538548	NPAS4	266743	0.05	trans
rs17113131	chr12	74564573	NPAS4	266743	0.05	trans
rs1344796	chr12	76397104	NPAS4	266743	0.17	trans
rs12302525	chr12	89726424	NPAS4	266743	0.08	trans
rs7296098	chr12	113228993	NPAS4	266743	0	trans
rs11833075	chr12	122114592	NPAS4	266743	0.04	trans
rs3803214	chr13	25740255	NPAS4	266743	0	trans
rs4497566	chr13	51694324	NPAS4	266743	0.03	trans
rs9574766	chr13	81723606	NPAS4	266743	0.19	trans
snp_a-4196949		0	NPAS4	266743	0.16	trans
rs7161226	chr14	88327803	NPAS4	266743	0.03	trans
rs1885073	chr14	104357181	NPAS4	266743	0.14	trans
rs4465541	chr14	105016846	NPAS4	266743	0.12	trans
rs17761129	chr15	24262387	NPAS4	266743	0.04	trans
rs4777108	chr15	69383464	NPAS4	266743	0	trans
rs9635390	chr15	90809632	NPAS4	266743	0.09	trans
rs8047151	chr16	17209696	NPAS4	266743	9.199E-9	trans
rs4271578	chr16	17213886	NPAS4	266743	4.972E-7	trans
rs7200513	chr16	17219474	NPAS4	266743	1.557E-8	trans
rs3829495	chr16	17221986	NPAS4	266743	2.621E-11	trans
rs7193763	chr16	17225534	NPAS4	266743	1.178E-5	trans
rs1867231	chr17	13678834	NPAS4	266743	0.01	trans
rs17817797	chr17	53332496	NPAS4	266743	0.11	trans
rs9646596	chr18	53049211	NPAS4	266743	6.997E-4	trans
rs17594526	chr18	53058237	NPAS4	266743	0.01	trans
rs17594665	chr18	53063718	NPAS4	266743	0.12	trans
rs11152369	chr18	53066327	NPAS4	266743	0.02	trans
rs1469489	chr18	57228488	NPAS4	266743	0.08	trans
rs9319807	chr18	68766779	NPAS4	266743	7.428E-4	trans
rs1942464	chr18	70509877	NPAS4	266743	0.13	trans
rs1991826	chr19	23705538	NPAS4	266743	0.14	trans
rs6417634	chr20	6408617	NPAS4	266743	0.12	trans
rs6085552	chr20	6409004	NPAS4	266743	0.15	trans
rs6109425	chr20	12443786	NPAS4	266743	0.18	trans
rs6026122	chr20	56769083	NPAS4	266743	0.18	trans
rs235980	chr21	28537426	NPAS4	266743	0.09	trans
rs134028	chr22	28048448	NPAS4	266743	0.07	trans
rs16978981	chrX	13538144	NPAS4	266743	6.383E-5	trans
rs4825301	chrX	19476433	NPAS4	266743	0.17	trans
rs7879159	chrX	19481591	NPAS4	266743	0	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.

No co-expressed genes in brain regions

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
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
NIKOLSKY BREAST CANCER 11Q12 Q14 AMPLICON	158	93	All SZGR 2.0 genes in this pathway
MARSON BOUND BY FOXP3 UNSTIMULATED	1229	713	All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3 UNMETHYLATED	536	296	All SZGR 2.0 genes in this pathway
MIKKELSEN IPS WITH HCP H3K27ME3	102	76	All SZGR 2.0 genes in this pathway
MIKKELSEN MEF HCP WITH H3 UNMETHYLATED	228	119	All SZGR 2.0 genes in this pathway
MARTENS BOUND BY PML RARA FUSION	456	287	All SZGR 2.0 genes in this pathway

Gene Page: NPAS4