SZGR2

Summary ?

GeneID	6602
Symbol	SMARCD1
Synonyms	BAF60A\|CRACD1\|Rsc6p
Description	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1
Reference	MIM:601735\|HGNC:HGNC:11106\|Ensembl:ENSG00000066117\|HPRD:03438\|Vega:OTTHUMG00000150194
Gene type	protein-coding
Map location	12q13-q14
Pascal p-value	3.415E-4
Sherlock p-value	0.371
Support	Chromatin Remodeling Genes

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.1006

Section I. Genetics and epigenetics annotation

Section II. Transcriptome annotation

General gene expression (GTEx)

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
DENND5A	0.82	0.77
CYTSB	0.82	0.81
RNF130	0.80	0.76
SPG20	0.79	0.80
JAM3	0.79	0.76
COL4A5	0.78	0.79
GLTP	0.77	0.80
LASS2	0.77	0.75
CHD1L	0.77	0.75
MOSPD2	0.76	0.77

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AC087071.1	-0.43	-0.38
FAM159B	-0.43	-0.40
RP9P	-0.41	-0.37
AF347015.21	-0.38	-0.14
AC135724.1	-0.37	-0.30
IL32	-0.37	-0.24
SPDYA	-0.37	-0.33
AC027807.2	-0.36	-0.31
AC120053.1	-0.34	-0.28
SPINK8	-0.32	-0.31

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0003713	transcription coactivator activity	TAS		8804307
GO:0032947	protein complex scaffold	IDA		12917342
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0006357	regulation of transcription from RNA polymerase II promoter	TAS		8804307
GO:0048096	chromatin-mediated maintenance of transcription	IMP		12917342
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005634	nucleus	IEA		-
GO:0005654	nucleoplasm	TAS		8804307
GO:0005730	nucleolus	IDA		18029348
GO:0016585	chromatin remodeling complex	IDA		12917342

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
BAZ1B	WBSCR10 \| WBSCR9 \| WSTF	bromodomain adjacent to zinc finger domain, 1B	-	HPRD,BioGRID	12837248
CALCOCO2	MGC17318 \| NDP52	calcium binding and coiled-coil domain 2	Two-hybrid	BioGRID	16189514
CCDC85B	DIPA	coiled-coil domain containing 85B	Two-hybrid	BioGRID	16189514
ESR1	DKFZp686N23123 \| ER \| ESR \| ESRA \| Era \| NR3A1	estrogen receptor 1	Reconstituted Complex	BioGRID	12917342
FOS	AP-1 \| C-FOS	v-fos FBJ murine osteosarcoma viral oncogene homolog	-	HPRD	11053448
GATA1	ERYF1 \| GF-1 \| GF1 \| NFE1	GATA binding protein 1 (globin transcription factor 1)	Reconstituted Complex	BioGRID	11018012
ING1	p24ING1c \| p33 \| p33ING1 \| p33ING1b \| p47 \| p47ING1a	inhibitor of growth family, member 1	Affinity Capture-MS	BioGRID	11784859
JUN	AP-1 \| AP1 \| c-Jun	jun oncogene	-	HPRD	11053448
KLF1	EKLF	Kruppel-like factor 1 (erythroid)	Reconstituted Complex	BioGRID	11018012
KRT15	CK15 \| K15 \| K1CO	keratin 15	Two-hybrid	BioGRID	16189514
LDOC1	BCUR1 \| Mar7 \| Mart7	leucine zipper, down-regulated in cancer 1	Two-hybrid	BioGRID	16189514
NR1H4	BAR \| FXR \| HRR-1 \| HRR1 \| MGC163445 \| RIP14	nuclear receptor subfamily 1, group H, member 4	Reconstituted Complex	BioGRID	12917342
NR3C1	GCCR \| GCR \| GR \| GRL	nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)	-	HPRD,BioGRID	12917342
PGR	NR3C3 \| PR	progesterone receptor	Reconstituted Complex	BioGRID	12917342
SMARCA4	BAF190 \| BRG1 \| FLJ39786 \| SNF2 \| SNF2-BETA \| SNF2L4 \| SNF2LB \| SWI2 \| hSNF2b	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	Affinity Capture-Western	BioGRID	12917342
SMARCC1	BAF155 \| CRACC1 \| Rsc8 \| SRG3 \| SWI3	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	Affinity Capture-Western	BioGRID	12917342
SMARCC2	BAF170 \| CRACC2 \| Rsc8	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	Affinity Capture-Western	BioGRID	12917342
TNIP2	ABIN-2 \| ABIN2 \| FLIP1 \| KLIP \| MGC4289	TNFAIP3 interacting protein 2	-	HPRD	12753905
TNIP2	ABIN-2 \| ABIN2 \| FLIP1 \| KLIP \| MGC4289	TNFAIP3 interacting protein 2	ABIN-2 interacts with BAF60a.	BIND	12753905
USHBP1	AIEBP \| FLJ38709 \| FLJ90681 \| MCC2	Usher syndrome 1C binding protein 1	Two-hybrid	BioGRID	16189514

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
PID REG GR PATHWAY	82	60	All SZGR 2.0 genes in this pathway
PARENT MTOR SIGNALING UP	567	375	All SZGR 2.0 genes in this pathway
GINESTIER BREAST CANCER ZNF217 AMPLIFIED DN	335	193	All SZGR 2.0 genes in this pathway
GINESTIER BREAST CANCER 20Q13 AMPLIFICATION DN	180	101	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
LOPEZ MBD TARGETS	957	597	All SZGR 2.0 genes in this pathway
LIU NASOPHARYNGEAL CARCINOMA	70	38	All SZGR 2.0 genes in this pathway
GOTZMANN EPITHELIAL TO MESENCHYMAL TRANSITION UP	69	55	All SZGR 2.0 genes in this pathway
BENPORATH CYCLING GENES	648	385	All SZGR 2.0 genes in this pathway
FAELT B CLL WITH VH3 21 UP	44	30	All SZGR 2.0 genes in this pathway
BANDRES RESPONSE TO CARMUSTIN WITHOUT MGMT 24HR UP	14	10	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP	1691	1088	All SZGR 2.0 genes in this pathway
BANDRES RESPONSE TO CARMUSTIN WITHOUT MGMT 48HR UP	18	13	All SZGR 2.0 genes in this pathway
BANDRES RESPONSE TO CARMUSTIN MGMT 48HR UP	18	13	All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 6HR UP	953	554	All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 24HR DN	1011	592	All SZGR 2.0 genes in this pathway
YAUCH HEDGEHOG SIGNALING PARACRINE UP	149	85	All SZGR 2.0 genes in this pathway
YAGI AML WITH T 8 21 TRANSLOCATION	368	247	All SZGR 2.0 genes in this pathway
SETLUR PROSTATE CANCER TMPRSS2 ERG FUSION UP	67	48	All SZGR 2.0 genes in this pathway
HOSHIDA LIVER CANCER SUBCLASS S1	237	159	All SZGR 2.0 genes in this pathway
BANDRES RESPONSE TO CARMUSTIN MGMT 24HR UP	9	5	All SZGR 2.0 genes in this pathway
SASSON RESPONSE TO GONADOTROPHINS DN	87	66	All SZGR 2.0 genes in this pathway
SASSON RESPONSE TO FORSKOLIN DN	88	68	All SZGR 2.0 genes in this pathway
WHITFIELD CELL CYCLE G2 M	216	124	All SZGR 2.0 genes in this pathway
PURBEY TARGETS OF CTBP1 NOT SATB1 DN	448	282	All SZGR 2.0 genes in this pathway
DELACROIX RAR BOUND ES	462	273	All SZGR 2.0 genes in this pathway
RATTENBACHER BOUND BY CELF1	467	251	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	1592	1598	m8	hsa-miR-101	UACAGUACUGUGAUAACUGAAG
miR-122	846	852	1A	hsa-miR-122a	UGGAGUGUGACAAUGGUGUUUGU
miR-122	846	852	1A	hsa-miR-122a	UGGAGUGUGACAAUGGUGUUUGU
miR-133	1575	1581	1A	hsa-miR-133a	UUGGUCCCCUUCAACCAGCUGU
miR-133	1575	1581	1A	hsa-miR-133b	UUGGUCCCCUUCAACCAGCUA
miR-148/152	974	980	1A	hsa-miR-148a	UCAGUGCACUACAGAACUUUGU
				hsa-miR-152^brain	UCAGUGCAUGACAGAACUUGGG
				hsa-miR-148b	UCAGUGCAUCACAGAACUUUGU
miR-150	1242	1248	1A	hsa-miR-150	UCUCCCAACCCUUGUACCAGUG
miR-150	1242	1248	1A	hsa-miR-150	UCUCCCAACCCUUGUACCAGUG
miR-199	1448	1455	1A,m8	hsa-miR-199a	CCCAGUGUUCAGACUACCUGUUC
miR-199	1448	1455	1A,m8	hsa-miR-199b	CCCAGUGUUUAGACUAUCUGUUC
miR-200bc/429	634	640	m8	hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
miR-21	425	432	1A,m8	hsa-miR-21^brain	UAGCUUAUCAGACUGAUGUUGA
miR-21	425	432	1A,m8	hsa-miR-590	GAGCUUAUUCAUAAAAGUGCAG
miR-214	591	597	m8	hsa-miR-214^brain	ACAGCAGGCACAGACAGGCAG
miR-214	591	597	m8	hsa-miR-214^brain	ACAGCAGGCACAGACAGGCAG
miR-223	1300	1307	1A,m8	hsa-miR-223	UGUCAGUUUGUCAAAUACCCC
miR-370	1104	1111	1A,m8	hsa-miR-370^brain	GCCUGCUGGGGUGGAACCUGG
miR-490	1182	1188	m8	hsa-miR-490	CAACCUGGAGGACUCCAUGCUG
miR-491	1319	1325	m8	hsa-miR-491^brain	AGUGGGGAACCCUUCCAUGAGGA
miR-7	1178	1184	1A	hsa-miR-7^SZ	UGGAAGACUAGUGAUUUUGUUG
miR-7	1178	1184	1A	hsa-miR-7^SZ	UGGAAGACUAGUGAUUUUGUUG
miR-99/100	897	903	1A	hsa-miR-99a^brain	AACCCGUAGAUCCGAUCUUGUG
				hsa-miR-100^brain	AACCCGUAGAUCCGAACUUGUG
				hsa-miR-99b^brain	CACCCGUAGAACCGACCUUGCG

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: SMARCD1