SZGR2

Summary ?

GeneID	22941
Symbol	SHANK2
Synonyms	AUTS17\|CORTBP1\|CTTNBP1\|ProSAP1\|SHANK\|SPANK-3
Description	SH3 and multiple ankyrin repeat domains 2
Reference	MIM:603290\|HGNC:HGNC:14295\|Ensembl:ENSG00000162105\|HPRD:04479\|Vega:OTTHUMG00000154615
Gene type	protein-coding
Map location	11q13.2
Pascal p-value	0.028
Sherlock p-value	0.191
Fetal beta	0.605
DMG	1 (# studies)
eGene	Myers' cis & trans
Support	PROTEIN CLUSTERING G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL G2Cdb.human_BAYES-COLLINS-MOUSE-PSD-CONSENSUS G2Cdb.humanNRC CompositeSet Darnell FMRP targets Potential synaptic genes

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
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).	2
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
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.061

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg26025487	11	70674245	SHANK2	1.175E-4	0.375	0.029	DMG:Wockner_2014
cg16456980	11	70714131	SHANK2	2.874E-4	-0.49	0.039	DMG:Wockner_2014

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs16894557	chr6	28999825	SHANK2	22941		0.02		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
ADNP	0.95	0.96
CYTSA	0.95	0.96
UBR5	0.94	0.95
LATS1	0.94	0.96
MGA	0.94	0.94
ZNF518B	0.94	0.97
NSD1	0.94	0.96
MED1	0.94	0.96
ARID2	0.94	0.95
HMGXB4	0.94	0.95

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AF347015.31	-0.70	-0.88
FXYD1	-0.70	-0.88
HLA-F	-0.69	-0.76
AIFM3	-0.69	-0.76
MT-CO2	-0.69	-0.88
TSC22D4	-0.68	-0.79
S100B	-0.68	-0.82
AF347015.27	-0.68	-0.84
C5orf53	-0.68	-0.74
IFI27	-0.67	-0.85

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0030160	GKAP/Homer scaffold activity	NAS	Synap (GO term level: 6)	10506216
GO:0005515	protein binding	IPI		11583995
GO:0005515	protein binding	NAS		-
GO:0017124	SH3 domain binding	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007242	intracellular signaling cascade	NAS		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0045211	postsynaptic membrane	IEA	Synap, Neurotransmitter (GO term level: 5)	-
GO:0045202	synapse	IEA	neuron, Synap, Neurotransmitter, Glial (GO term level: 2)	-
GO:0005737	cytoplasm	IEA		-
GO:0005886	plasma membrane	IEA		-
GO:0030054	cell junction	IEA		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
ARHGEF7	BETA-PIX \| COOL1 \| DKFZp686C12170 \| DKFZp761K1021 \| KIAA0142 \| KIAA0412 \| Nbla10314 \| P50 \| P50BP \| P85 \| P85COOL1 \| P85SPR \| PAK3 \| PIXB	Rho guanine nucleotide exchange factor (GEF) 7	-	HPRD,BioGRID	12626503
BAI2	-	brain-specific angiogenesis inhibitor 2	-	HPRD,BioGRID	10964907
BAIAP2	BAP2 \| IRSP53	BAI1-associated protein 2	-	HPRD	12504591
CTTN	EMS1 \| FLJ34459	cortactin	-	HPRD,BioGRID	9742101
DLG4	FLJ97752 \| FLJ98574 \| PSD95 \| SAP90	discs, large homolog 4 (Drosophila)	-	HPRD,BioGRID	10527873
DLGAP1	DAP-1 \| DAP-1-ALPHA \| DAP-1-BETA \| GKAP \| MGC88156 \| SAPAP1 \| hGKAP	discs, large (Drosophila) homolog-associated protein 1	-	HPRD,BioGRID	10527873
DLGAP2	DAP2 \| SAPAP2	discs, large (Drosophila) homolog-associated protein 2	Two-hybrid	BioGRID	10527873
DLGAP3	DAP3 \| SAPAP3	discs, large (Drosophila) homolog-associated protein 3	Two-hybrid	BioGRID	10527873
DLGAP4	DAP4 \| KIAA0964 \| MGC131862 \| RP5-977B1.6 \| SAPAP4	discs, large (Drosophila) homolog-associated protein 4	Two-hybrid	BioGRID	10527873
DNM2	CMTDI1 \| CMTDIB \| DI-CMTB \| DYN2 \| DYNII	dynamin 2	-	HPRD,BioGRID	11583995
DYNLL1	DLC1 \| DLC8 \| DNCL1 \| DNCLC1 \| LC8 \| LC8a \| MGC126137 \| MGC126138 \| PIN \| hdlc1	dynein, light chain, LC8-type 1	Affinity Capture-Western	BioGRID	10844022
DYNLL2	DNCL1B \| Dlc2 \| MGC17810	dynein, light chain, LC8-type 2	Affinity Capture-Western	BioGRID	10844022
LPHN1	CIRL1 \| CL1 \| LEC2	latrophilin 1	-	HPRD,BioGRID	10964907
LPHN2	CIRL2 \| CL2 \| LEC1 \| LPHH1	latrophilin 2	-	HPRD,BioGRID	10964907
MYO5A	GS1 \| MYH12 \| MYO5 \| MYR12	myosin VA (heavy chain 12, myoxin)	Affinity Capture-Western	BioGRID	10844022
SSTR2	-	somatostatin receptor 2	-	HPRD	10373412

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
SCHUETZ BREAST CANCER DUCTAL INVASIVE DN	84	53	All SZGR 2.0 genes in this pathway
FRASOR TAMOXIFEN RESPONSE UP	51	36	All SZGR 2.0 genes in this pathway
CHARAFE BREAST CANCER LUMINAL VS BASAL UP	380	215	All SZGR 2.0 genes in this pathway
CHARAFE BREAST CANCER LUMINAL VS MESENCHYMAL UP	450	256	All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA UP	1821	933	All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA POORLY DIFFERENTIATED DN	805	505	All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA ANAPLASTIC DN	537	339	All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA DN	77	52	All SZGR 2.0 genes in this pathway
GOZGIT ESR1 TARGETS DN	781	465	All SZGR 2.0 genes in this pathway
ODONNELL METASTASIS UP	82	58	All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS UP	1037	673	All SZGR 2.0 genes in this pathway
NIKOLSKY BREAST CANCER 11Q12 Q14 AMPLICON	158	93	All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT REJECTED VS OK DN	546	351	All SZGR 2.0 genes in this pathway
MOREAUX MULTIPLE MYELOMA BY TACI UP	412	249	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN	1237	837	All SZGR 2.0 genes in this pathway
RODWELL AGING KIDNEY NO BLOOD DN	150	93	All SZGR 2.0 genes in this pathway
RODWELL AGING KIDNEY DN	145	88	All SZGR 2.0 genes in this pathway
RODWELL AGING KIDNEY UP	487	303	All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 2	473	224	All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 5	482	296	All SZGR 2.0 genes in this pathway
MASSARWEH TAMOXIFEN RESISTANCE UP	578	341	All SZGR 2.0 genes in this pathway
HAN SATB1 TARGETS UP	395	249	All SZGR 2.0 genes in this pathway
HAN SATB1 TARGETS DN	442	275	All SZGR 2.0 genes in this pathway
MEISSNER ES ICP WITH H3K4ME3	34	17	All SZGR 2.0 genes in this pathway
MEISSNER NPC ICP WITH H3 UNMETHYLATED	24	15	All SZGR 2.0 genes in this pathway
MEISSNER BRAIN ICP WITH H3K4ME3	32	17	All SZGR 2.0 genes in this pathway
MIKKELSEN MCV6 ICP WITH H3K27ME3	74	46	All SZGR 2.0 genes in this pathway
NAKAYAMA SOFT TISSUE TUMORS PCA1 DN	74	47	All SZGR 2.0 genes in this pathway
MARTENS TRETINOIN RESPONSE UP	857	456	All SZGR 2.0 genes in this pathway
ACOSTA PROLIFERATION INDEPENDENT MYC TARGETS DN	116	74	All SZGR 2.0 genes in this pathway
KRIEG HYPOXIA NOT VIA KDM3A	770	480	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	2883	2889	1A	hsa-miR-101	UACAGUACUGUGAUAACUGAAG
miR-101	2883	2889	1A	hsa-miR-101	UACAGUACUGUGAUAACUGAAG
miR-124/506	4847	4853	m8	hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
				hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
				hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
				hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
miR-130/301	3358	3364	m8	hsa-miR-130a^brain	CAGUGCAAUGUUAAAAGGGCAU
				hsa-miR-301	CAGUGCAAUAGUAUUGUCAAAGC
				hsa-miR-130b^brain	CAGUGCAAUGAUGAAAGGGCAU
				hsa-miR-454-3p	UAGUGCAAUAUUGCUUAUAGGGUUU
miR-137	2716	2723	1A,m8	hsa-miR-137	UAUUGCUUAAGAAUACGCGUAG
miR-142-5p	3326	3333	1A,m8	hsa-miR-142-5p	CAUAAAGUAGAAAGCACUAC
miR-144	3404	3410	1A	hsa-miR-144	UACAGUAUAGAUGAUGUACUAG
miR-144	3404	3410	1A	hsa-miR-144	UACAGUAUAGAUGAUGUACUAG
miR-186	1673	1679	1A	hsa-miR-186	CAAAGAAUUCUCCUUUUGGGCUU
miR-19	3357	3363	m8	hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
miR-19	3357	3363	m8	hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
miR-218	1713	1720	1A,m8	hsa-miR-218^brain	UUGUGCUUGAUCUAACCAUGU
miR-218	1713	1720	1A,m8	hsa-miR-218^brain	UUGUGCUUGAUCUAACCAUGU
miR-221/222	4824	4830	m8	hsa-miR-221^brain	AGCUACAUUGUCUGCUGGGUUUC
miR-221/222	4824	4830	m8	hsa-miR-222^brain	AGCUACAUCUGGCUACUGGGUCUC
miR-23	3045	3051	m8	hsa-miR-23a^brain	AUCACAUUGCCAGGGAUUUCC
miR-23	3045	3051	m8	hsa-miR-23b^brain	AUCACAUUGCCAGGGAUUACC
miR-323	3045	3051	1A	hsa-miR-323^brain	GCACAUUACACGGUCGACCUCU
miR-324-3p	648	654	m8	hsa-miR-324-3p	CCACUGCCCCAGGUGCUGCUGG
miR-33	4879	4885	m8	hsa-miR-33	GUGCAUUGUAGUUGCAUUG
miR-33	4879	4885	m8	hsa-miR-33b	GUGCAUUGCUGUUGCAUUGCA
miR-374	1574	1580	1A	hsa-miR-374	UUAUAAUACAACCUGAUAAGUG
miR-381	3385	3391	m8	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-495	2874	2880	1A	hsa-miR-495^brain	AAACAAACAUGGUGCACUUCUUU
miR-7	2293	2300	1A,m8	hsa-miR-7^SZ	UGGAAGACUAGUGAUUUUGUUG
miR-9	127	133	1A	hsa-miR-9^SZ	UCUUUGGUUAUCUAGCUGUAUGA

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: SHANK2