SZGR2

Summary ?

GeneID	4884
Symbol	NPTX1
Synonyms	NP1
Description	neuronal pentraxin 1
Reference	MIM:602367\|HGNC:HGNC:7952\|Ensembl:ENSG00000171246\|HPRD:03843\|Vega:OTTHUMG00000177607
Gene type	protein-coding
Map location	17q25.3
Pascal p-value	4.757E-5
Sherlock p-value	0.911
DMG	1 (# studies)
eGene	Cerebellum Nucleus accumbens basal ganglia Myers' cis & trans
Support	INTRACELLULAR SIGNAL TRANSDUCTION G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL G2Cdb.human_clathrin G2Cdb.human_Synaptosome Potential synaptic genes

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
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: 2

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg23752000	17	78442298	NPTX1	1.83E-5	-0.573	0.016	DMG:Wockner_2014

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs8081537	chr17	77708263	NPTX1	4884	0.12	cis
rs9515552	chr13	89948963	NPTX1	4884	0.14	trans
rs7321205	chr13	89949815	NPTX1	4884	0.09	trans

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
ITGAV	0.82	0.82
ARHGAP5	0.80	0.78
GPM6B	0.79	0.76
IL6ST	0.79	0.77
KIAA0494	0.79	0.78
NEBL	0.78	0.75
ALDH5A1	0.77	0.77
PCGF5	0.76	0.72
SLC30A1	0.76	0.76
SPRED1	0.76	0.77

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
RP9P	-0.41	-0.51
SNHG12	-0.41	-0.48
ST20	-0.39	-0.43
MRPL52	-0.37	-0.38
BCL7C	-0.37	-0.42
RPL35	-0.36	-0.44
IL32	-0.35	-0.35
AL022328.1	-0.35	-0.36
RPL36	-0.35	-0.43
AC008763.1	-0.35	-0.36

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005509	calcium ion binding	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007417	central nervous system development	TAS	Brain (GO term level: 6)	8884281
GO:0007268	synaptic transmission	TAS	neuron, Synap, Neurotransmitter (GO term level: 6)	8884281
GO:0006810	transport	TAS		8884281
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0031410	cytoplasmic vesicle	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
NAKAMURA TUMOR ZONE PERIPHERAL VS CENTRAL DN	634	384	All SZGR 2.0 genes in this pathway
ZHONG RESPONSE TO AZACITIDINE AND TSA UP	183	119	All SZGR 2.0 genes in this pathway
HUTTMANN B CLL POOR SURVIVAL UP	276	187	All SZGR 2.0 genes in this pathway
TONKS TARGETS OF RUNX1 RUNX1T1 FUSION HSC UP	185	126	All SZGR 2.0 genes in this pathway
GOZGIT ESR1 TARGETS UP	149	84	All SZGR 2.0 genes in this pathway
CHEBOTAEV GR TARGETS DN	120	73	All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN UP	1142	669	All SZGR 2.0 genes in this pathway
GRAESSMANN RESPONSE TO MC AND DOXORUBICIN UP	612	367	All SZGR 2.0 genes in this pathway
PEREZ TP63 TARGETS	355	243	All SZGR 2.0 genes in this pathway
PEREZ TP53 AND TP63 TARGETS	205	145	All SZGR 2.0 genes in this pathway
LIANG HEMATOPOIESIS STEM CELL NUMBER LARGE VS TINY DN	45	24	All SZGR 2.0 genes in this pathway
LIANG HEMATOPOIESIS STEM CELL NUMBER SMALL VS HUGE DN	33	22	All SZGR 2.0 genes in this pathway
SCHLESINGER METHYLATED DE NOVO IN CANCER	88	64	All SZGR 2.0 genes in this pathway
GROSS HYPOXIA VIA HIF1A DN	110	78	All SZGR 2.0 genes in this pathway
NUYTTEN NIPP1 TARGETS DN	848	527	All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS UP	1037	673	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
JI METASTASIS REPRESSED BY STK11	27	17	All SZGR 2.0 genes in this pathway
SWEET KRAS TARGETS UP	84	51	All SZGR 2.0 genes in this pathway
NADLER HYPERGLYCEMIA AT OBESITY	58	35	All SZGR 2.0 genes in this pathway
PETROVA ENDOTHELIUM LYMPHATIC VS BLOOD DN	162	102	All SZGR 2.0 genes in this pathway
MODY HIPPOCAMPUS POSTNATAL	63	50	All SZGR 2.0 genes in this pathway
WANG SMARCE1 TARGETS DN	371	218	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 14HR DN	298	200	All SZGR 2.0 genes in this pathway
MCCLUNG DELTA FOSB TARGETS 2WK	48	36	All SZGR 2.0 genes in this pathway
DEBIASI APOPTOSIS BY REOVIRUS INFECTION DN	287	208	All SZGR 2.0 genes in this pathway
SATO SILENCED BY METHYLATION IN PANCREATIC CANCER 1	419	273	All SZGR 2.0 genes in this pathway
JIANG AGING CEREBRAL CORTEX DN	54	43	All SZGR 2.0 genes in this pathway
DURCHDEWALD SKIN CARCINOGENESIS DN	264	168	All SZGR 2.0 genes in this pathway
LIN NPAS4 TARGETS DN	68	48	All SZGR 2.0 genes in this pathway
BLUM RESPONSE TO SALIRASIB DN	342	220	All SZGR 2.0 genes in this pathway
LIANG HEMATOPOIESIS STEM CELL NUMBER QTL	17	10	All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 2	86	50	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 2HR DN	49	33	All SZGR 2.0 genes in this pathway
MARTENS TRETINOIN RESPONSE UP	857	456	All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS OLIGODENDROCYTE NUMBER CORR UP	756	494	All SZGR 2.0 genes in this pathway
KIM BIPOLAR DISORDER OLIGODENDROCYTE DENSITY CORR UP	682	440	All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS CALB1 CORR UP	548	370	All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS CONFLUENT	567	365	All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE LATE	1137	655	All SZGR 2.0 genes in this pathway
FORTSCHEGGER PHF8 TARGETS UP	279	155	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-1/206	3262	3268	1A	hsa-miR-1	UGGAAUGUAAAGAAGUAUGUA
				hsa-miR-206^SZ	UGGAAUGUAAGGAAGUGUGUGG
				hsa-miR-613	AGGAAUGUUCCUUCUUUGCC
miR-101	2958	2964	1A	hsa-miR-101	UACAGUACUGUGAUAACUGAAG
miR-128	2624	2630	m8	hsa-miR-128a	UCACAGUGAACCGGUCUCUUUU
miR-128	2624	2630	m8	hsa-miR-128b	UCACAGUGAACCGGUCUCUUUC
miR-130/301	2734	2740	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-133	3311	3317	m8	hsa-miR-133a	UUGGUCCCCUUCAACCAGCUGU
miR-133	3311	3317	m8	hsa-miR-133b	UUGGUCCCCUUCAACCAGCUA
miR-138	3183	3189	m8	hsa-miR-138^brain	AGCUGGUGUUGUGAAUC
miR-139	2959	2966	1A,m8	hsa-miR-139^brain	UCUACAGUGCACGUGUCU
miR-144	2958	2964	1A	hsa-miR-144	UACAGUAUAGAUGAUGUACUAG
miR-148/152	2735	2742	1A,m8	hsa-miR-148a	UCAGUGCACUACAGAACUUUGU
				hsa-miR-152^brain	UCAGUGCAUGACAGAACUUGGG
				hsa-miR-148b	UCAGUGCAUCACAGAACUUUGU
miR-182	3661	3668	1A,m8	hsa-miR-182	UUUGGCAAUGGUAGAACUCACA
miR-200bc/429	2943	2950	1A,m8	hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
miR-204/211	3597	3604	1A,m8	hsa-miR-204^brain	UUCCCUUUGUCAUCCUAUGCCU
miR-204/211	3597	3604	1A,m8	hsa-miR-211	UUCCCUUUGUCAUCCUUCGCCU
miR-210	127	133	m8	hsa-miR-210	CUGUGCGUGUGACAGCGGCUGA
miR-25/32/92/363/367	3584	3590	m8	hsa-miR-25^brain	CAUUGCACUUGUCUCGGUCUGA
				hsa-miR-32	UAUUGCACAUUACUAAGUUGC
				hsa-miR-92	UAUUGCACUUGUCCCGGCCUG
				hsa-miR-367	AAUUGCACUUUAGCAAUGGUGA
				hsa-miR-92b^SZ	UAUUGCACUCGUCCCGGCCUC
miR-34/449	1600	1606	m8	hsa-miR-34a^brain	UGGCAGUGUCUUAGCUGGUUGUU
				hsa-miR-34c	AGGCAGUGUAGUUAGCUGAUUGC
				hsa-miR-449	UGGCAGUGUAUUGUUAGCUGGU
				hsa-miR-449b	AGGCAGUGUAUUGUUAGCUGGC
miR-346	1623	1629	1A	hsa-miR-346^brain	UGUCUGCCCGCAUGCCUGCCUCU
miR-34b	1601	1607	m8	hsa-miR-34b	UAGGCAGUGUCAUUAGCUGAUUG
miR-369-3p	2945	2951	m8	hsa-miR-369-3p	AAUAAUACAUGGUUGAUCUUU
miR-539	2950	2956	m8	hsa-miR-539	GGAGAAAUUAUCCUUGGUGUGU
miR-9	3776	3782	m8	hsa-miR-9^SZ	UCUUUGGUUAUCUAGCUGUAUGA
miR-96	3662	3668	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: NPTX1