SZGR2

Summary ?

GeneID	27173
Symbol	SLC39A1
Synonyms	ZIP1\|ZIRTL
Description	solute carrier family 39 member 1
Reference	MIM:604740\|HGNC:HGNC:12876\|Ensembl:ENSG00000143570\|HPRD:11984\|Vega:OTTHUMG00000037158
Gene type	protein-coding
Map location	1q21
Sherlock p-value	0.383
Fetal beta	-0.022
DMG	1 (# studies)
eGene	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
GSMA_I	Genome scan meta-analysis	Psr: 0.0235
GSMA_IIA	Genome scan meta-analysis (All samples)	Psr: 0.00814

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg14747580	1	153936275	SLC39A1	2.15E-8	-0.006	7.29E-6	DMG:Jaffe_2016

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs4501739	chrX	35960848	SLC39A1	27173		0.14		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
UNC119	0.92	0.91
TBCB	0.91	0.91
EBP	0.90	0.91
DALRD3	0.90	0.91
RNF25	0.90	0.91
DGUOK	0.89	0.89
FNDC4	0.89	0.91
ITPA	0.89	0.91
STK19	0.89	0.91
EMD	0.89	0.88

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AF347015.8	-0.74	-0.77
AF347015.27	-0.73	-0.76
AF347015.26	-0.72	-0.80
MT-CYB	-0.72	-0.77
AF347015.33	-0.72	-0.76
MT-CO2	-0.72	-0.73
AF347015.15	-0.71	-0.77
AF347015.2	-0.71	-0.78
AF347015.31	-0.69	-0.72
MT-ATP8	-0.66	-0.79

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005385	zinc ion transmembrane transporter activity	IEA		-
GO:0008270	zinc ion binding	IEA		-
GO:0046873	metal ion transmembrane transporter activity	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0030001	metal ion transport	IEA		-
GO:0006829	zinc ion transport	IEA		-
GO:0006811	ion transport	IEA		-
GO:0015674	di-, tri-valent inorganic cation transport	TAS		10610721
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005789	endoplasmic reticulum membrane	IEA		-
GO:0005624	membrane fraction	TAS		10610721
GO:0005783	endoplasmic reticulum	IEA		-
GO:0016020	membrane	IEA		-
GO:0016021	integral to membrane	TAS		10610721
GO:0005886	plasma membrane	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
REACTOME TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES	413	270	All SZGR 2.0 genes in this pathway
REACTOME SLC MEDIATED TRANSMEMBRANE TRANSPORT	241	157	All SZGR 2.0 genes in this pathway
REACTOME TRANSPORT OF GLUCOSE AND OTHER SUGARS BILE SALTS AND ORGANIC ACIDS METAL IONS AND AMINE COMPOUNDS	89	54	All SZGR 2.0 genes in this pathway
REACTOME ZINC TRANSPORTERS	15	9	All SZGR 2.0 genes in this pathway
REACTOME METAL ION SLC TRANSPORTERS	22	13	All SZGR 2.0 genes in this pathway
MULLIGHAN NPM1 MUTATED SIGNATURE 1 UP	276	165	All SZGR 2.0 genes in this pathway
MULLIGHAN NPM1 MUTATED SIGNATURE 2 UP	139	83	All SZGR 2.0 genes in this pathway
MULLIGHAN NPM1 SIGNATURE 3 UP	341	197	All SZGR 2.0 genes in this pathway
PATIL LIVER CANCER	747	453	All SZGR 2.0 genes in this pathway
LOCKWOOD AMPLIFIED IN LUNG CANCER	214	139	All SZGR 2.0 genes in this pathway
BENPORATH SOX2 TARGETS	734	436	All SZGR 2.0 genes in this pathway
GEORGES TARGETS OF MIR192 AND MIR215	893	528	All SZGR 2.0 genes in this pathway
ZHOU TNF SIGNALING 30MIN	54	36	All SZGR 2.0 genes in this pathway
MARSON BOUND BY FOXP3 UNSTIMULATED	1229	713	All SZGR 2.0 genes in this pathway
RIZKI TUMOR INVASIVENESS 3D UP	210	124	All SZGR 2.0 genes in this pathway
MCCABE BOUND BY HOXC6	469	239	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE UP	863	514	All SZGR 2.0 genes in this pathway
KRIEG HYPOXIA NOT VIA KDM3A	770	480	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-182	815	821	1A	hsa-miR-182	UUUGGCAAUGGUAGAACUCACA
miR-182	815	821	1A	hsa-miR-182	UUUGGCAAUGGUAGAACUCACA
miR-218	605	611	m8	hsa-miR-218^brain	UUGUGCUUGAUCUAACCAUGU
miR-223	939	945	m8	hsa-miR-223	UGUCAGUUUGUCAAAUACCCC
miR-96	575	582	1A,m8	hsa-miR-96^brain	UUUGGCACUAGCACAUUUUUGC
miR-96	575	582	1A,m8	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: SLC39A1