SZGR2

Summary ?

GeneID	8467
Symbol	SMARCA5
Synonyms	ISWI\|SNF2H\|WCRF135\|hISWI\|hSNF2H
Description	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5
Reference	MIM:603375\|HGNC:HGNC:11101\|Ensembl:ENSG00000153147\|HPRD:04538\|Vega:OTTHUMG00000161474
Gene type	protein-coding
Map location	4q31.1-q31.2
Pascal p-value	0.005
Sherlock p-value	0.857
Fetal beta	0.897
DMG	1 (# studies)
eGene	Myers' cis & trans
Support	Ascano FMRP targets Chromatin Remodeling Genes

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
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.	1

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg16091845	4	144434637	SMARCA5		-0.022	0.67	DMG:Nishioka_2013

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs6599250	chr3	38784028	SMARCA5	8467	0.17	trans
rs4491879	chr3	189373908	SMARCA5	8467	0.12	trans
rs6046959	chr20	20588433	SMARCA5	8467	0.18	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
MMADHC	0.94	0.94
DRG1	0.93	0.89
PSMD14	0.93	0.90
PPA1	0.93	0.90
MRPL3	0.92	0.90
TXNL1	0.92	0.90
OLA1	0.92	0.90
CCT4	0.92	0.94
ATP5A1	0.92	0.90
MRPS35	0.92	0.90

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AF347015.26	-0.73	-0.76
AF347015.8	-0.73	-0.74
AF347015.2	-0.73	-0.73
MT-CYB	-0.73	-0.73
MT-CO2	-0.73	-0.71
AF347015.33	-0.72	-0.74
AF347015.15	-0.72	-0.74
AF347015.31	-0.70	-0.69
AF347015.27	-0.68	-0.70
AF347015.18	-0.65	-0.74

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
ALB	DKFZp779N1935 \| PRO0883 \| PRO0903 \| PRO1341	albumin	SNF2H interacts with the Albumin gene.	BIND	15616580
BAZ1A	ACF1 \| DKFZp586E0518 \| FLJ14383 \| WALp1 \| WCRF180 \| hACF1	bromodomain adjacent to zinc finger domain, 1A	-	HPRD,BioGRID	10655480 \|10880450 \|11980720
BAZ1A	ACF1 \| DKFZp586E0518 \| FLJ14383 \| WALp1 \| WCRF180 \| hACF1	bromodomain adjacent to zinc finger domain, 1A	SNF2H interacts with hACF1.	BIND	15780937
BAZ1B	WBSCR10 \| WBSCR9 \| WSTF	bromodomain adjacent to zinc finger domain, 1B	-	HPRD,BioGRID	11980720
BAZ2A	DKFZp781B109 \| FLJ13768 \| FLJ13780 \| FLJ45876 \| KIAA0314 \| TIP5 \| WALp3	bromodomain adjacent to zinc finger domain, 2A	-	HPRD,BioGRID	11532953
CHD3	Mi-2a \| Mi2-ALPHA \| ZFH	chromodomain helicase DNA binding protein 3	Co-purification	BioGRID	12198550
CHRAC1	CHARC1 \| CHARC15 \| CHRAC15 \| YCL1	chromatin accessibility complex 1	-	HPRD	12434153
CHRAC1	CHARC1 \| CHARC15 \| CHRAC15 \| YCL1	chromatin accessibility complex 1	Affinity Capture-Western Co-purification	BioGRID	10880450
DNMT3B	ICF \| M.HsaIIIB	DNA (cytosine-5-)-methyltransferase 3 beta	Co-purification	BioGRID	15148359
DNMT3B	ICF \| M.HsaIIIB	DNA (cytosine-5-)-methyltransferase 3 beta	DNMT3B interacts with hSNF2H.	BIND	15120635
H3F3A	H3.3A \| H3F3 \| MGC87782 \| MGC87783	H3 histone, family 3A	H3F3A (Histone 3) interacts with SMARCA5 (SNF2H).	BIND	15616580
HDAC2	RPD3 \| YAF1	histone deacetylase 2	SMARCA5 (SNF2h) interacts with HDAC2.	BIND	15775975
HDAC2	RPD3 \| YAF1	histone deacetylase 2	Co-purification	BioGRID	12198550
HNF1A	HNF1 \| LFB1 \| MODY3 \| TCF1	HNF1 homeobox A	SNF2H interacts with the HNF-1 gene.	BIND	15616580
PHC3	DKFZp313K1221 \| EDR3 \| FLJ12729 \| FLJ12967 \| HPH3 \| MGC88144	polyhomeotic homolog 3 (Drosophila)	-	HPRD	12167701
POLE3	CHARAC17 \| CHRAC17 \| YBL1 \| p17	polymerase (DNA directed), epsilon 3 (p17 subunit)	Affinity Capture-Western Co-purification	BioGRID	10880450
RAD21	FLJ25655 \| FLJ40596 \| HR21 \| HRAD21 \| KIAA0078 \| MCD1 \| NXP1 \| SCC1 \| hHR21	RAD21 homolog (S. pombe)	-	HPRD,BioGRID	12198550
RBBP4	NURF55 \| RBAP48	retinoblastoma binding protein 4	Co-purification	BioGRID	12198550
SATB1	-	SATB homeobox 1	-	HPRD,BioGRID	12374985
SMC1A	CDLS2 \| DKFZp686L19178 \| DXS423E \| KIAA0178 \| MGC138332 \| SB1.8 \| SMC1 \| SMC1L1 \| SMC1alpha \| SMCB	structural maintenance of chromosomes 1A	Co-purification	BioGRID	12198550
SMC3	BAM \| BMH \| CDLS3 \| CSPG6 \| HCAP \| SMC3L1	structural maintenance of chromosomes 3	Co-purification	BioGRID	12198550

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
REACTOME CELL CYCLE	421	253	All SZGR 2.0 genes in this pathway
REACTOME CHROMOSOME MAINTENANCE	122	80	All SZGR 2.0 genes in this pathway
REACTOME DEPOSITION OF NEW CENPA CONTAINING NUCLEOSOMES AT THE CENTROMERE	64	43	All SZGR 2.0 genes in this pathway
ONKEN UVEAL MELANOMA UP	783	507	All SZGR 2.0 genes in this pathway
DAVICIONI MOLECULAR ARMS VS ERMS UP	332	228	All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP	1382	904	All SZGR 2.0 genes in this pathway
TIEN INTESTINE PROBIOTICS 24HR UP	557	331	All SZGR 2.0 genes in this pathway
BARIS THYROID CANCER DN	59	45	All SZGR 2.0 genes in this pathway
SCHLOSSER SERUM RESPONSE DN	712	443	All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 DN	855	609	All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK	1652	1023	All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK	1442	892	All SZGR 2.0 genes in this pathway
PUJANA CHEK2 PCC NETWORK	779	480	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 6HR DN	514	330	All SZGR 2.0 genes in this pathway
SCHAEFFER SOX9 TARGETS IN PROSTATE DEVELOPMENT DN	45	33	All SZGR 2.0 genes in this pathway
STARK PREFRONTAL CORTEX 22Q11 DELETION UP	195	138	All SZGR 2.0 genes in this pathway
SHEN SMARCA2 TARGETS UP	424	268	All SZGR 2.0 genes in this pathway
MORI IMMATURE B LYMPHOCYTE DN	90	55	All SZGR 2.0 genes in this pathway
ZHAN MULTIPLE MYELOMA CD1 AND CD2 UP	89	51	All SZGR 2.0 genes in this pathway
WANG SMARCE1 TARGETS DN	371	218	All SZGR 2.0 genes in this pathway
MARTINEZ RESPONSE TO TRABECTEDIN DN	271	175	All SZGR 2.0 genes in this pathway
RIGGINS TAMOXIFEN RESISTANCE DN	220	147	All SZGR 2.0 genes in this pathway
IWANAGA CARCINOGENESIS BY KRAS UP	170	107	All SZGR 2.0 genes in this pathway
ZHANG BREAST CANCER PROGENITORS UP	425	253	All SZGR 2.0 genes in this pathway
ZHANG TLX TARGETS 36HR DN	185	116	All SZGR 2.0 genes in this pathway
WINNEPENNINCKX MELANOMA METASTASIS UP	162	86	All SZGR 2.0 genes in this pathway
ONGUSAHA BRCA1 TARGETS DN	14	9	All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 3 DN	918	550	All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS DN	882	538	All SZGR 2.0 genes in this pathway
FEVR CTNNB1 TARGETS DN	553	343	All SZGR 2.0 genes in this pathway

Gene Page: SMARCA5