SZGR2

Summary ?

GeneID	4862
Symbol	NPAS2
Synonyms	MOP4\|PASD4\|bHLHe9
Description	neuronal PAS domain protein 2
Reference	MIM:603347\|HGNC:HGNC:7895\|Ensembl:ENSG00000170485\|HPRD:09137\|Vega:OTTHUMG00000130675
Gene type	protein-coding
Map location	2q11.2
Pascal p-value	0.015
Support	CompositeSet Darnell FMRP targets

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: 0.0004
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: 1

Section I. Genetics and epigenetics annotation

Section II. Transcriptome annotation

General gene expression (GTEx)

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
MARCH7	0.97	0.97
KLHL9	0.97	0.97
CTDSPL2	0.95	0.96
RBMXL1	0.95	0.95
FSD1L	0.95	0.95
KIAA1430	0.95	0.96
NCBP1	0.95	0.96
STX7	0.94	0.96
RAB10	0.94	0.96
XRCC5	0.94	0.95

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
HLA-F	-0.68	-0.77
AC018755.7	-0.68	-0.76
FXYD1	-0.68	-0.87
MT-CO2	-0.67	-0.86
AIFM3	-0.67	-0.76
AF347015.33	-0.66	-0.83
AF347015.31	-0.66	-0.84
AF347015.27	-0.66	-0.82
MT-CYB	-0.65	-0.83
C5orf53	-0.65	-0.71

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0004871	signal transducer activity	IEA		-
GO:0003700	transcription factor activity	TAS		9012850
GO:0051879	Hsp90 protein binding	IDA		9079689
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007417	central nervous system development	TAS	Brain (GO term level: 6)	9012850
GO:0006355	regulation of transcription, DNA-dependent	IEA		-
GO:0007165	signal transduction	IEA		-
GO:0042745	circadian sleep/wake cycle	IEA		-
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	IGI		9576906
GO:0048511	rhythmic process	IEA		-
GO:0045475	locomotor rhythm	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005634	nucleus	IEA		-
GO:0005667	transcription factor complex	IPI		9576906

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG CIRCADIAN RHYTHM MAMMAL	13	13	All SZGR 2.0 genes in this pathway
PID CIRCADIAN PATHWAY	16	15	All SZGR 2.0 genes in this pathway
REACTOME BMAL1 CLOCK NPAS2 ACTIVATES CIRCADIAN EXPRESSION	36	27	All SZGR 2.0 genes in this pathway
REACTOME PPARA ACTIVATES GENE EXPRESSION	104	72	All SZGR 2.0 genes in this pathway
REACTOME RORA ACTIVATES CIRCADIAN EXPRESSION	24	17	All SZGR 2.0 genes in this pathway
REACTOME CIRCADIAN REPRESSION OF EXPRESSION BY REV ERBA	23	16	All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF LIPIDS AND LIPOPROTEINS	478	302	All SZGR 2.0 genes in this pathway
REACTOME FATTY ACID TRIACYLGLYCEROL AND KETONE BODY METABOLISM	168	115	All SZGR 2.0 genes in this pathway
REACTOME CIRCADIAN CLOCK	53	40	All SZGR 2.0 genes in this pathway
ONKEN UVEAL MELANOMA UP	783	507	All SZGR 2.0 genes in this pathway
SENESE HDAC1 TARGETS UP	457	269	All SZGR 2.0 genes in this pathway
SENESE HDAC3 TARGETS UP	501	327	All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE FIMA UP	544	308	All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 3 DN	229	142	All SZGR 2.0 genes in this pathway
HERNANDEZ ABERRANT MITOSIS BY DOCETACEL 2NM UP	81	57	All SZGR 2.0 genes in this pathway
LIAO METASTASIS	539	324	All SZGR 2.0 genes in this pathway
KOYAMA SEMA3B TARGETS UP	292	168	All SZGR 2.0 genes in this pathway
BENPORATH NANOG TARGETS	988	594	All SZGR 2.0 genes in this pathway
BENPORATH SUZ12 TARGETS	1038	678	All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3	1118	744	All SZGR 2.0 genes in this pathway
MANALO HYPOXIA UP	207	145	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN	1237	837	All SZGR 2.0 genes in this pathway
DAZARD RESPONSE TO UV NHEK DN	318	220	All SZGR 2.0 genes in this pathway
DAZARD UV RESPONSE CLUSTER G6	153	112	All SZGR 2.0 genes in this pathway
MARTINEZ RESPONSE TO TRABECTEDIN DN	271	175	All SZGR 2.0 genes in this pathway
DOUGLAS BMI1 TARGETS UP	566	371	All SZGR 2.0 genes in this pathway
KONDO EZH2 TARGETS	245	148	All SZGR 2.0 genes in this pathway
HINATA NFKB TARGETS FIBROBLAST UP	84	60	All SZGR 2.0 genes in this pathway
HAN SATB1 TARGETS UP	395	249	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
CAIRO LIVER DEVELOPMENT UP	166	105	All SZGR 2.0 genes in this pathway
KYNG WERNER SYNDROM AND NORMAL AGING DN	225	124	All SZGR 2.0 genes in this pathway
MIKKELSEN NPC HCP WITH H3K27ME3	341	243	All SZGR 2.0 genes in this pathway
DUTERTRE ESTRADIOL RESPONSE 24HR DN	505	328	All SZGR 2.0 genes in this pathway
IVANOVSKA MIR106B TARGETS	90	56	All SZGR 2.0 genes in this pathway
PEDRIOLI MIR31 TARGETS DN	418	245	All SZGR 2.0 genes in this pathway
ACEVEDO FGFR1 TARGETS IN PROSTATE CANCER MODEL UP	289	184	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-17-5p/20/93.mr/106/519.d	523	529	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
				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-19	492	499	1A,m8	hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
miR-19	492	499	1A,m8	hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
miR-199	723	730	1A,m8	hsa-miR-199a	CCCAGUGUUCAGACUACCUGUUC
miR-199	723	730	1A,m8	hsa-miR-199b	CCCAGUGUUUAGACUAUCUGUUC
miR-218	782	789	1A,m8	hsa-miR-218^brain	UUGUGCUUGAUCUAACCAUGU
miR-320	29	36	1A,m8	hsa-miR-320	AAAAGCUGGGUUGAGAGGGCGAA
miR-335	380	387	1A,m8	hsa-miR-335^brain	UCAAGAGCAAUAACGAAAAAUGU
miR-495	1007	1013	1A	hsa-miR-495^brain	AAACAAACAUGGUGCACUUCUUU

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: NPAS2