SZGR2

Summary ?

GeneID	6594
Symbol	SMARCA1
Synonyms	ISWI\|NURF140\|SNF2L\|SNF2L1\|SNF2LB\|SNF2LT\|SWI\|SWI2\|hSNF2L
Description	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1
Reference	MIM:300012\|HGNC:HGNC:11097\|Ensembl:ENSG00000102038\|HPRD:02055\|Vega:OTTHUMG00000022370
Gene type	protein-coding
Map location	Xq25
Sherlock p-value	0.938
Fetal beta	0.543
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
PMID:cooccur	High-throughput literature-search	Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenias	Click to show details
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 2

Section I. Genetics and epigenetics annotation

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
SAP30BP	0.88	0.89
PRKRIP1	0.86	0.87
PDAP1	0.86	0.89
RBM8A	0.86	0.91
FTSJ3	0.85	0.87
EXOSC2	0.85	0.86
ODF2	0.85	0.89
XRCC1	0.85	0.86
ILKAP	0.85	0.86
SNRPA1	0.84	0.85

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AF347015.27	-0.73	-0.79
AF347015.31	-0.73	-0.78
MT-CO2	-0.70	-0.76
MT-CYB	-0.69	-0.74
AF347015.2	-0.69	-0.78
AF347015.33	-0.68	-0.73
AF347015.8	-0.68	-0.74
AF347015.15	-0.68	-0.75
AF347015.21	-0.64	-0.74
HLA-F	-0.64	-0.66

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0000166	nucleotide binding	IEA		-
GO:0003677	DNA binding	IEA		-
GO:0005515	protein binding	IPI		14609955
GO:0005524	ATP binding	IEA		-
GO:0004386	helicase activity	TAS		1408766
GO:0016787	hydrolase activity	IEA		-
GO:0008094	DNA-dependent ATPase activity	IDA		14609955
GO:0030528	transcription regulator activity	IMP		14609955
GO:0031491	nucleosome binding	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007420	brain development	IMP	Brain (GO term level: 7)	14609955
GO:0030182	neuron differentiation	ISS	neuron (GO term level: 8)	-
GO:0006355	regulation of transcription, DNA-dependent	IEA		-
GO:0006350	transcription	IEA		-
GO:0043193	positive regulation of gene-specific transcription	IMP		14609955
GO:0043044	ATP-dependent chromatin remodeling	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005634	nucleus	IDA		14609955
GO:0005737	cytoplasm	IDA		18029348
GO:0016585	chromatin remodeling complex	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
ONKEN UVEAL MELANOMA DN	526	357	All SZGR 2.0 genes in this pathway
VECCHI GASTRIC CANCER EARLY DN	367	220	All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 1 DN	242	165	All SZGR 2.0 genes in this pathway
TONKS TARGETS OF RUNX1 RUNX1T1 FUSION HSC UP	185	126	All SZGR 2.0 genes in this pathway
SENESE HDAC1 TARGETS DN	260	143	All SZGR 2.0 genes in this pathway
JAATINEN HEMATOPOIETIC STEM CELL UP	316	190	All SZGR 2.0 genes in this pathway
ENK UV RESPONSE KERATINOCYTE DN	485	334	All SZGR 2.0 genes in this pathway
CHEBOTAEV GR TARGETS DN	120	73	All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL TGFB1 TARGETS UP	169	127	All SZGR 2.0 genes in this pathway
XU HGF TARGETS REPRESSED BY AKT1 DN	95	58	All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 DN	855	609	All SZGR 2.0 genes in this pathway
RICKMAN METASTASIS UP	344	180	All SZGR 2.0 genes in this pathway
ROZANOV MMP14 CORRELATED	11	9	All SZGR 2.0 genes in this pathway
ROZANOV MMP14 TARGETS UP	266	171	All SZGR 2.0 genes in this pathway
MAGRANGEAS MULTIPLE MYELOMA IGLL VS IGLK UP	42	24	All SZGR 2.0 genes in this pathway
ZHAN MULTIPLE MYELOMA MF UP	47	27	All SZGR 2.0 genes in this pathway
KAAB FAILED HEART ATRIUM DN	141	99	All SZGR 2.0 genes in this pathway
SATO SILENCED BY METHYLATION IN PANCREATIC CANCER 2	50	34	All SZGR 2.0 genes in this pathway
KAYO AGING MUSCLE UP	244	165	All SZGR 2.0 genes in this pathway
XU GH1 EXOGENOUS TARGETS DN	120	69	All SZGR 2.0 genes in this pathway
YIH RESPONSE TO ARSENITE C1	24	14	All SZGR 2.0 genes in this pathway
SATO SILENCED BY METHYLATION IN PANCREATIC CANCER 1	419	273	All SZGR 2.0 genes in this pathway
HELLER SILENCED BY METHYLATION UP	282	183	All SZGR 2.0 genes in this pathway
AMUNDSON POOR SURVIVAL AFTER GAMMA RADIATION 8G	95	62	All SZGR 2.0 genes in this pathway
AMUNDSON POOR SURVIVAL AFTER GAMMA RADIATION 2G	171	96	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER UP	973	570	All SZGR 2.0 genes in this pathway
ALONSO METASTASIS EMT UP	36	24	All SZGR 2.0 genes in this pathway
ALONSO METASTASIS UP	198	128	All SZGR 2.0 genes in this pathway
HAN SATB1 TARGETS UP	395	249	All SZGR 2.0 genes in this pathway
BOYAULT LIVER CANCER SUBCLASS G1 UP	113	70	All SZGR 2.0 genes in this pathway
HOSHIDA LIVER CANCER SUBCLASS S2	115	74	All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA CLASSES UP	605	377	All SZGR 2.0 genes in this pathway
CAIRO LIVER DEVELOPMENT UP	166	105	All SZGR 2.0 genes in this pathway
KYNG WERNER SYNDROM AND NORMAL AGING DN	225	124	All SZGR 2.0 genes in this pathway
GREGORY SYNTHETIC LETHAL WITH IMATINIB	145	83	All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS UP	745	475	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-101	347	354	1A,m8	hsa-miR-101	UACAGUACUGUGAUAACUGAAG
miR-128	615	621	1A	hsa-miR-128a	UCACAGUGAACCGGUCUCUUUU
miR-128	615	621	1A	hsa-miR-128b	UCACAGUGAACCGGUCUCUUUC
miR-134	74	80	1A	hsa-miR-134^brain	UGUGACUGGUUGACCAGAGGG
miR-144	718	724	m8	hsa-miR-144	UACAGUAUAGAUGAUGUACUAG
miR-144	718	724	m8	hsa-miR-144	UACAGUAUAGAUGAUGUACUAG
miR-27	615	621	m8	hsa-miR-27a^brain	UUCACAGUGGCUAAGUUCCGC
miR-27	615	621	m8	hsa-miR-27b^brain	UUCACAGUGGCUAAGUUCUGC
miR-369-3p	481	487	m8	hsa-miR-369-3p	AAUAAUACAUGGUUGAUCUUU
miR-376c	431	437	m8	hsa-miR-376c	AACAUAGAGGAAAUUCCACG
miR-410	277	283	1A	hsa-miR-410	AAUAUAACACAGAUGGCCUGU
miR-494	491	497	1A	hsa-miR-494^brain	UGAAACAUACACGGGAAACCUCUU
miR-503	447	453	m8	hsa-miR-503	UAGCAGCGGGAACAGUUCUGCAG

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: SMARCA1