SZGR2

Summary ?

GeneID	79065
Symbol	ATG9A
Synonyms	APG9L1\|MGD3208\|mATG9
Description	autophagy related 9A
Reference	MIM:612204\|HGNC:HGNC:22408\|Ensembl:ENSG00000198925\|HPRD:07979\|Vega:OTTHUMG00000154557
Gene type	protein-coding
Map location	2q35
Pascal p-value	2.321E-5
Sherlock p-value	4.203E-5
Fetal beta	-0.067
eGene	Cerebellum Myers' cis & trans
Support	CompositeSet Darnell FMRP targets

Gene in Data Sources

Gene set name	Method of gene set	Description
CV:PGCnp	Genome-wide Association Study	GWAS
GSMA_IIA	Genome scan meta-analysis (All samples)	Psr: 0.00916
GSMA_IIE	Genome scan meta-analysis (European-ancestry samples)	Psr: 0.01016

Section I. Genetics and epigenetics annotation

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs4425711	chr7	54637269	ATG9A	79065		0.17		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
VPS35	0.87	0.85
MUDENG	0.87	0.85
HIAT1	0.86	0.84
SLC30A9	0.86	0.84
NIPA2	0.85	0.82
PIAS2	0.85	0.83
YIPF5	0.85	0.84
KIAA1715	0.85	0.86
AKAP10	0.85	0.86
PSMD5	0.85	0.82

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
MT-CO2	-0.69	-0.62
AF347015.8	-0.69	-0.62
AF347015.21	-0.69	-0.59
MT-CYB	-0.67	-0.60
AF347015.2	-0.66	-0.57
AF347015.31	-0.66	-0.60
AF347015.33	-0.65	-0.58
AF347015.26	-0.65	-0.57
AF347015.15	-0.65	-0.59
AF347015.18	-0.64	-0.62

Section III. Gene Ontology annotation

Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0000045	autophagic vacuole formation	IMP		15755735
GO:0006914	autophagy	IEA		-
GO:0015031	protein transport	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005737	cytoplasm	IEA		-
GO:0005776	autophagic vacuole	IEA		-
GO:0016020	membrane	IEA		-
GO:0016021	integral to membrane	IEA		-
GO:0031410	cytoplasmic vesicle	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
HORIUCHI WTAP TARGETS DN	310	188	All SZGR 2.0 genes in this pathway
SENESE HDAC3 TARGETS DN	536	332	All SZGR 2.0 genes in this pathway
DOUGLAS BMI1 TARGETS UP	566	371	All SZGR 2.0 genes in this pathway
MITSIADES RESPONSE TO APLIDIN UP	439	257	All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA HAPTOTAXIS DN	668	419	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
LINSLEY MIR16 TARGETS	206	127	All SZGR 2.0 genes in this pathway
KRIEG HYPOXIA NOT VIA KDM3A	770	480	All SZGR 2.0 genes in this pathway
MIZUSHIMA AUTOPHAGOSOME FORMATION	19	15	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-28	925	931	1A	hsa-miR-28^brain	AAGGAGCUCACAGUCUAUUGAG
miR-29	251	258	1A,m8	hsa-miR-29a^SZ	UAGCACCAUCUGAAAUCGGUU
				hsa-miR-29b^SZ	UAGCACCAUUUGAAAUCAGUGUU
				hsa-miR-29c^SZ	UAGCACCAUUUGAAAUCGGU
miR-338	914	920	m8	hsa-miR-338^brain	UCCAGCAUCAGUGAUUUUGUUGA
miR-34/449	286	292	1A	hsa-miR-34a^brain	UGGCAGUGUCUUAGCUGGUUGUU
				hsa-miR-34c	AGGCAGUGUAGUUAGCUGAUUGC
				hsa-miR-449	UGGCAGUGUAUUGUUAGCUGGU
				hsa-miR-449b	AGGCAGUGUAUUGUUAGCUGGC
miR-96	362	368	m8	hsa-miR-96^brain	UUUGGCACUAGCACAUUUUUGC
miR-96	362	368	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: ATG9A