SZGR2

Summary ?

GeneID	10092
Symbol	ARPC5
Synonyms	ARC16\|dJ127C7.3\|p16-Arc
Description	actin related protein 2/3 complex subunit 5
Reference	MIM:604227\|HGNC:HGNC:708\|HPRD:11969\|
Gene type	protein-coding
Map location	1q25.3
Sherlock p-value	0.647
Fetal beta	0.925
DMG	2 (# studies)
Support	STRUCTURAL PLASTICITY

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.	4
DMG:Nishioka_2013	Genome-wide DNA methylation analysis	The authors investigated the methylation profiles of DNA in peripheral blood cells from 18 patients with first-episode schizophrenia (FESZ) and from 15 normal controls.	4
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).	4
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 1

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg26018965	1	183604789	ARPC5;RGL1	2.628E-4	-0.272	0.038	DMG:Wockner_2014
cg27155653	1	183604774	ARPC5		-0.033	0.27	DMG:Nishioka_2013
cg12737363	1	183604674	ARPC5	2.24E-10	-0.029	5.98E-7	DMG:Jaffe_2016
cg27155653	1	183604774	ARPC5	3.34E-8	-0.012	9.98E-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
SUFU	0.97	0.95
C14orf118	0.96	0.95
RNF38	0.96	0.96
RFX7	0.96	0.96
ZNF398	0.95	0.96
ZNF317	0.95	0.97
DCAF5	0.95	0.97
DCP1A	0.95	0.95
RRP1B	0.95	0.95
PRRC1	0.95	0.95

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
C5orf53	-0.71	-0.77
AF347015.31	-0.71	-0.88
MT-CO2	-0.70	-0.89
AIFM3	-0.70	-0.77
FXYD1	-0.70	-0.88
S100B	-0.69	-0.83
AF347015.33	-0.69	-0.85
AF347015.27	-0.69	-0.86
HLA-F	-0.69	-0.75
IFI27	-0.68	-0.84

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0003779	actin binding	IEA		-
GO:0005515	protein binding	IPI		17353931
GO:0005200	structural constituent of cytoskeleton	TAS		9230079
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0006928	cell motion	TAS		9230079
GO:0030036	actin cytoskeleton organization	TAS		9359840
GO:0030833	regulation of actin filament polymerization	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0042995	cell projection	IEA	axon (GO term level: 4)	-
GO:0005856	cytoskeleton	IEA		-
GO:0005737	cytoplasm	TAS		9359840
GO:0005885	Arp2/3 protein complex	TAS		9230079

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG FC GAMMA R MEDIATED PHAGOCYTOSIS	97	71	All SZGR 2.0 genes in this pathway
KEGG REGULATION OF ACTIN CYTOSKELETON	216	144	All SZGR 2.0 genes in this pathway
KEGG PATHOGENIC ESCHERICHIA COLI INFECTION	59	36	All SZGR 2.0 genes in this pathway
BIOCARTA SALMONELLA PATHWAY	13	10	All SZGR 2.0 genes in this pathway
BIOCARTA MPR PATHWAY	34	28	All SZGR 2.0 genes in this pathway
BIOCARTA RHO PATHWAY	32	23	All SZGR 2.0 genes in this pathway
BIOCARTA CDC42RAC PATHWAY	16	13	All SZGR 2.0 genes in this pathway
BIOCARTA ACTINY PATHWAY	20	14	All SZGR 2.0 genes in this pathway
PID CDC42 PATHWAY	70	51	All SZGR 2.0 genes in this pathway
PID ERBB1 DOWNSTREAM PATHWAY	105	78	All SZGR 2.0 genes in this pathway
PID PDGFRB PATHWAY	129	103	All SZGR 2.0 genes in this pathway
PID RAC1 PATHWAY	54	37	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
SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN DN	584	395	All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK	1442	892	All SZGR 2.0 genes in this pathway
RICKMAN METASTASIS DN	261	155	All SZGR 2.0 genes in this pathway
BENPORATH OCT4 TARGETS	290	172	All SZGR 2.0 genes in this pathway
DORSAM HOXA9 TARGETS UP	35	25	All SZGR 2.0 genes in this pathway
LU IL4 SIGNALING	94	56	All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS	882	572	All SZGR 2.0 genes in this pathway
PENG GLUCOSE DEPRIVATION DN	169	112	All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT OK VS DONOR UP	555	346	All SZGR 2.0 genes in this pathway
REN ALVEOLAR RHABDOMYOSARCOMA DN	408	274	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN	1237	837	All SZGR 2.0 genes in this pathway
JIANG HYPOXIA CANCER	83	52	All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 1	528	324	All SZGR 2.0 genes in this pathway
ACEVEDO NORMAL TISSUE ADJACENT TO LIVER TUMOR UP	174	96	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER UP	973	570	All SZGR 2.0 genes in this pathway
WANG TUMOR INVASIVENESS UP	374	247	All SZGR 2.0 genes in this pathway
CHAUHAN RESPONSE TO METHOXYESTRADIOL DN	102	65	All SZGR 2.0 genes in this pathway
CHEN METABOLIC SYNDROM NETWORK	1210	725	All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 17	181	101	All SZGR 2.0 genes in this pathway
IKEDA MIR133 TARGETS UP	43	27	All SZGR 2.0 genes in this pathway
WAKABAYASHI ADIPOGENESIS PPARG BOUND 8D	658	397	All SZGR 2.0 genes in this pathway
ALFANO MYC TARGETS	239	156	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	865	871	m8	hsa-miR-124a	UUAAGGCACGCGGUGAAUGCCA
miR-124/506	865	871	1A	hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
miR-124/506	865	871	1A	hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
miR-141/200a	933	939	m8	hsa-miR-141	UAACACUGUCUGGUAAAGAUGG
miR-141/200a	933	939	m8	hsa-miR-200a	UAACACUGUCUGGUAACGAUGU
miR-145	459	465	m8	hsa-miR-145	GUCCAGUUUUCCCAGGAAUCCCUU
miR-190	148	155	1A,m8	hsa-miR-190	UGAUAUGUUUGAUAUAUUAGGU
miR-193	379	385	m8	hsa-miR-193a	AACUGGCCUACAAAGUCCCAG
miR-193	379	385	m8	hsa-miR-193b	AACUGGCCCUCAAAGUCCCGCUUU
miR-320	104	110	m8	hsa-miR-320	AAAAGCUGGGUUGAGAGGGCGAA

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: ARPC5