SZGR2

Summary ?

GeneID	80153
Symbol	EDC3
Synonyms	LSM16\|MRT50\|YJDC\|YJEFN2
Description	enhancer of mRNA decapping 3
Reference	MIM:609842\|HGNC:HGNC:26114\|Ensembl:ENSG00000179151\|HPRD:07954\|Vega:OTTHUMG00000142815
Gene type	protein-coding
Map location	15q24.1
Pascal p-value	0.66
Sherlock p-value	0.676
Fetal beta	0.629
DMG	1 (# studies)

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
Expression	Meta-analysis of gene expression	P value: 1.815

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg10986864	15	74988803	EDC3	1.66E-8	-0.013	6.09E-6	DMG:Jaffe_2016

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
TRMT2A	0.76	0.76
ZFP41	0.75	0.77
MZF1	0.74	0.74
RFNG	0.73	0.75
PSMG4	0.73	0.70
ARRDC1	0.72	0.71
CHKB	0.71	0.68
NARFL	0.71	0.70
ADCK5	0.71	0.69
CCDC130	0.71	0.71

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
MT-ATP8	-0.49	-0.51
AF347015.8	-0.48	-0.45
AF347015.31	-0.48	-0.45
MT-CYB	-0.47	-0.45
AF347015.27	-0.47	-0.45
AF347015.2	-0.46	-0.43
MT-CO2	-0.46	-0.43
AF347015.15	-0.46	-0.43
AF347015.21	-0.45	-0.48
AL139819.3	-0.45	-0.46

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005515	protein binding	IPI		16364915 \|17353931
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005737	cytoplasm	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG RNA DEGRADATION	59	37	All SZGR 2.0 genes in this pathway
REACTOME MRNA DECAY BY 5 TO 3 EXORIBONUCLEASE	15	10	All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF MRNA	284	128	All SZGR 2.0 genes in this pathway
REACTOME DEADENYLATION DEPENDENT MRNA DECAY	48	29	All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF RNA	330	155	All SZGR 2.0 genes in this pathway
CASORELLI ACUTE PROMYELOCYTIC LEUKEMIA DN	663	425	All SZGR 2.0 genes in this pathway
XU GH1 AUTOCRINE TARGETS UP	268	157	All SZGR 2.0 genes in this pathway
IWANAGA CARCINOGENESIS BY KRAS PTEN DN	353	226	All SZGR 2.0 genes in this pathway
ROME INSULIN TARGETS IN MUSCLE DN	204	114	All SZGR 2.0 genes in this pathway
PURBEY TARGETS OF CTBP1 AND SATB1 DN	180	116	All SZGR 2.0 genes in this pathway
WAKABAYASHI ADIPOGENESIS PPARG RXRA BOUND 8D	882	506	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-124.1	55	61	1A	hsa-miR-124a	UUAAGGCACGCGGUGAAUGCCA
miR-22	285	291	m8	hsa-miR-22^brain	AAGCUGCCAGUUGAAGAACUGU
miR-29	856	862	m8	hsa-miR-29a^SZ	UAGCACCAUCUGAAAUCGGUU
				hsa-miR-29b^SZ	UAGCACCAUUUGAAAUCAGUGUU
				hsa-miR-29c^SZ	UAGCACCAUUUGAAAUCGGU
miR-30-5p	271	278	1A,m8	hsa-miR-30a-5p	UGUAAACAUCCUCGACUGGAAG
				hsa-miR-30c^brain	UGUAAACAUCCUACACUCUCAGC
				hsa-miR-30d^SZ	UGUAAACAUCCCCGACUGGAAG
				hsa-miR-30b^SZ	UGUAAACAUCCUACACUCAGCU
				hsa-miR-30e-5p	UGUAAACAUCCUUGACUGGA
				hsa-miR-30a-5p	UGUAAACAUCCUCGACUGGAAG
				hsa-miR-30c^brain	UGUAAACAUCCUACACUCUCAGC
				hsa-miR-30d^SZ	UGUAAACAUCCCCGACUGGAAG
				hsa-miR-30b^SZ	UGUAAACAUCCUACACUCAGCU
				hsa-miR-30e-5p	UGUAAACAUCCUUGACUGGA
miR-342	119	125	1A	hsa-miR-342^brain	UCUCACACAGAAAUCGCACCCGUC

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: EDC3