SZGR2

Summary ?

GeneID	4836
Symbol	NMT1
Synonyms	NMT
Description	N-myristoyltransferase 1
Reference	MIM:160993\|HGNC:HGNC:7857\|Ensembl:ENSG00000136448\|HPRD:01187\|Vega:OTTHUMG00000180003
Gene type	protein-coding
Map location	17q21.31
Pascal p-value	0.01
Sherlock p-value	0.985
Fetal beta	-1.656
DMG	1 (# studies)
eGene	Putamen basal ganglia
Support	Ascano FMRP targets

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
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.0351

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg16080654	17	43176852	NMT1	5.725E-4	0.403	0.049	DMG:Wockner_2014

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs149804735	17	43349729	NMT1	ENSG00000136448.7	3.202E-6	0.04	211078	gtex_brain_putamen_basal
rs17685379	17	43352049	NMT1	ENSG00000136448.7	3.232E-6	0.04	213398	gtex_brain_putamen_basal
rs3785803	17	43361213	NMT1	ENSG00000136448.7	3.472E-6	0.04	222562	gtex_brain_putamen_basal
rs11079503	17	43365089	NMT1	ENSG00000136448.7	3.258E-6	0.04	226438	gtex_brain_putamen_basal
rs11574815	17	43365392	NMT1	ENSG00000136448.7	3.314E-6	0.04	226741	gtex_brain_putamen_basal
rs35518221	17	43365441	NMT1	ENSG00000136448.7	3.317E-6	0.04	226790	gtex_brain_putamen_basal
rs111882557	17	43377320	NMT1	ENSG00000136448.7	3.57E-6	0.04	238669	gtex_brain_putamen_basal
rs149586082	17	43377551	NMT1	ENSG00000136448.7	3.572E-6	0.04	238900	gtex_brain_putamen_basal
rs112969331	17	43378398	NMT1	ENSG00000136448.7	3.58E-6	0.04	239747	gtex_brain_putamen_basal
rs79442196	17	43379488	NMT1	ENSG00000136448.7	3.592E-6	0.04	240837	gtex_brain_putamen_basal
rs111244088	17	43379765	NMT1	ENSG00000136448.7	3.594E-6	0.04	241114	gtex_brain_putamen_basal
rs75911690	17	43380115	NMT1	ENSG00000136448.7	3.599E-6	0.04	241464	gtex_brain_putamen_basal
rs79789477	17	43380341	NMT1	ENSG00000136448.7	3.599E-6	0.04	241690	gtex_brain_putamen_basal
rs1476533	17	43383595	NMT1	ENSG00000136448.7	3.444E-6	0.04	244944	gtex_brain_putamen_basal
rs75184106	17	43385263	NMT1	ENSG00000136448.7	3.371E-6	0.04	246612	gtex_brain_putamen_basal
rs79039330	17	43385620	NMT1	ENSG00000136448.7	3.357E-6	0.04	246969	gtex_brain_putamen_basal

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
TSNAXIP1	0.85	0.64
WDR66	0.85	0.69
DLEC1	0.83	0.56
CCDC39	0.83	0.64
AC079354.2	0.83	0.62
C7orf63	0.83	0.65
DNAH2	0.82	0.59
LRP2BP	0.82	0.53
RPGR	0.82	0.55
ZBBX	0.82	0.61

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
TBR1	-0.34	-0.25
SOX5	-0.33	-0.16
AFF3	-0.32	-0.15
ID2	-0.32	-0.29
NEUROD2	-0.31	-0.21
PRDM8	-0.31	-0.21
BACH2	-0.31	-0.12
DAB1	-0.31	-0.14
TSHZ3	-0.31	-0.17
KCTD12	-0.31	-0.19

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0004379	glycylpeptide N-tetradecanoyltransferase activity	IEA		-
GO:0016740	transferase activity	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0001701	in utero embryonic development	IEA		-
GO:0006499	N-terminal protein myristoylation	NAS		-
GO:0009249	protein lipoylation	TAS		9506952
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005829	cytosol	EXP		11099414
GO:0005575	cellular_component	ND		-
GO:0005737	cytoplasm	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
REACTOME APOPTOSIS	148	94	All SZGR 2.0 genes in this pathway
REACTOME HIV INFECTION	207	122	All SZGR 2.0 genes in this pathway
REACTOME HIV LIFE CYCLE	125	69	All SZGR 2.0 genes in this pathway
REACTOME LATE PHASE OF HIV LIFE CYCLE	104	61	All SZGR 2.0 genes in this pathway
REACTOME INTRINSIC PATHWAY FOR APOPTOSIS	30	21	All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP	1382	904	All SZGR 2.0 genes in this pathway
KINSEY TARGETS OF EWSR1 FLII FUSION UP	1278	748	All SZGR 2.0 genes in this pathway
HAHTOLA SEZARY SYNDROM UP	98	58	All SZGR 2.0 genes in this pathway
ENK UV RESPONSE EPIDERMIS UP	293	179	All SZGR 2.0 genes in this pathway
CHIARADONNA NEOPLASTIC TRANSFORMATION KRAS DN	142	95	All SZGR 2.0 genes in this pathway
CHIARADONNA NEOPLASTIC TRANSFORMATION CDC25 DN	153	100	All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN DN	1781	1082	All SZGR 2.0 genes in this pathway
BERENJENO TRANSFORMED BY RHOA UP	536	340	All SZGR 2.0 genes in this pathway
SCHLOSSER SERUM RESPONSE DN	712	443	All SZGR 2.0 genes in this pathway
DAIRKEE TERT TARGETS UP	380	213	All SZGR 2.0 genes in this pathway
GRUETZMANN PANCREATIC CANCER UP	358	245	All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK	1652	1023	All SZGR 2.0 genes in this pathway
PUJANA CHEK2 PCC NETWORK	779	480	All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS UP	1037	673	All SZGR 2.0 genes in this pathway
WEI MYCN TARGETS WITH E BOX	795	478	All SZGR 2.0 genes in this pathway
RICKMAN METASTASIS UP	344	180	All SZGR 2.0 genes in this pathway
BENPORATH NANOG TARGETS	988	594	All SZGR 2.0 genes in this pathway
PENG LEUCINE DEPRIVATION DN	187	122	All SZGR 2.0 genes in this pathway
BECKER TAMOXIFEN RESISTANCE UP	50	36	All SZGR 2.0 genes in this pathway
PENG RAPAMYCIN RESPONSE DN	245	154	All SZGR 2.0 genes in this pathway
PENG GLUTAMINE DEPRIVATION DN	337	230	All SZGR 2.0 genes in this pathway
MOREAUX B LYMPHOCYTE MATURATION BY TACI DN	73	45	All SZGR 2.0 genes in this pathway
MOREAUX MULTIPLE MYELOMA BY TACI DN	172	107	All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS STEM CELL LONG TERM	302	191	All SZGR 2.0 genes in this pathway
SESTO RESPONSE TO UV C4	20	14	All SZGR 2.0 genes in this pathway
WANG CISPLATIN RESPONSE AND XPC DN	228	146	All SZGR 2.0 genes in this pathway
JIANG HYPOXIA NORMAL	311	205	All SZGR 2.0 genes in this pathway
TSENG IRS1 TARGETS UP	113	71	All SZGR 2.0 genes in this pathway
KRASNOSELSKAYA ILF3 TARGETS DN	46	38	All SZGR 2.0 genes in this pathway
WELCSH BRCA1 TARGETS DN	141	92	All SZGR 2.0 genes in this pathway
KYNG DNA DAMAGE BY 4NQO OR UV	63	44	All SZGR 2.0 genes in this pathway
KYNG DNA DAMAGE DN	195	135	All SZGR 2.0 genes in this pathway
ACEVEDO NORMAL TISSUE ADJACENT TO LIVER TUMOR DN	354	216	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER DN	540	340	All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS DN	366	257	All SZGR 2.0 genes in this pathway
AGUIRRE PANCREATIC CANCER COPY NUMBER UP	298	174	All SZGR 2.0 genes in this pathway
SWEET LUNG CANCER KRAS UP	491	316	All SZGR 2.0 genes in this pathway
SWEET KRAS ONCOGENIC SIGNATURE	89	56	All SZGR 2.0 genes in this pathway
KUROKAWA LIVER CANCER EARLY RECURRENCE UP	12	9	All SZGR 2.0 genes in this pathway
DANG REGULATED BY MYC DN	253	192	All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 13	172	107	All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE LATE	1137	655	All SZGR 2.0 genes in this pathway
WAKABAYASHI ADIPOGENESIS PPARG RXRA BOUND 8D	882	506	All SZGR 2.0 genes in this pathway
WAKABAYASHI ADIPOGENESIS PPARG RXRA BOUND WITH H4K20ME1 MARK	145	82	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-124/506	1060	1066	m8	hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
miR-124/506	1060	1066	m8	hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
miR-138	2898	2904	1A	hsa-miR-138^brain	AGCUGGUGUUGUGAAUC
miR-143	3338	3344	1A	hsa-miR-143^brain	UGAGAUGAAGCACUGUAGCUCA
miR-204/211	251	257	1A	hsa-miR-204^brain	UUCCCUUUGUCAUCCUAUGCCU
miR-204/211	251	257	1A	hsa-miR-211	UUCCCUUUGUCAUCCUUCGCCU
miR-214	263	269	1A	hsa-miR-214^brain	ACAGCAGGCACAGACAGGCAG
miR-330	570	576	1A	hsa-miR-330^brain	GCAAAGCACACGGCCUGCAGAGA
miR-362	379	385	m8	hsa-miR-362	AAUCCUUGGAACCUAGGUGUGAGU
miR-369-3p	331	337	1A	hsa-miR-369-3p	AAUAAUACAUGGUUGAUCUUU
miR-374	331	337	m8	hsa-miR-374	UUAUAAUACAACCUGAUAAGUG
miR-410	333	339	1A	hsa-miR-410	AAUAUAACACAGAUGGCCUGU
miR-493-5p	374	381	1A,m8	hsa-miR-493-5p	UUGUACAUGGUAGGCUUUCAUU
miR-7	742	748	1A	hsa-miR-7^SZ	UGGAAGACUAGUGAUUUUGUUG
miR-9	1821	1828	1A,m8	hsa-miR-9^SZ	UCUUUGGUUAUCUAGCUGUAUGA

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: NMT1