SZGR2

Summary ?

GeneID	6608
Symbol	SMO
Synonyms	FZD11\|Gx\|SMOH
Description	smoothened, frizzled class receptor
Reference	MIM:601500\|HGNC:HGNC:11119\|Ensembl:ENSG00000128602\|HPRD:03294\|Vega:OTTHUMG00000158421
Gene type	protein-coding
Map location	7q32.3
Pascal p-value	0.744
Fetal beta	1.173
DMG	1 (# studies)
eGene	Myers' cis & trans

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.	1
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: 1

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg19015909	7	128828512	SMO	6.97E-8	0.006	1.69E-5	DMG:Jaffe_2016

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs11080561	chr18	12257229	SMO	6608		0		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
CD99L2	0.88	0.86
MAP7D2	0.87	0.87
PLEKHB2	0.87	0.86
AARS	0.86	0.85
DDHD2	0.86	0.85
MAP1A	0.86	0.84
RNF157	0.86	0.84
NSF	0.86	0.86
EHD3	0.86	0.85
ATP6V0A1	0.86	0.85

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
C1orf61	-0.42	-0.43
RPL35	-0.41	-0.47
IL32	-0.41	-0.38
SIGIRR	-0.41	-0.48
CLEC3B	-0.41	-0.47
BCL7C	-0.41	-0.51
FAM159B	-0.40	-0.60
AC006276.2	-0.40	-0.41
GNG11	-0.40	-0.33
RAMP2	-0.40	-0.46

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0004872	receptor activity	TAS		9422511
GO:0004930	G-protein coupled receptor activity	IEA		-
GO:0005515	protein binding	TAS		8906787
GO:0004926	non-G-protein coupled 7TM receptor activity	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0021953	central nervous system neuron differentiation	IEA	neuron (GO term level: 9)	-
GO:0001755	neural crest cell migration	IEA		-
GO:0001570	vasculogenesis	IEA		-
GO:0001649	osteoblast differentiation	IEA		-
GO:0002052	positive regulation of neuroblast proliferation	IEA		-
GO:0003007	heart morphogenesis	IEA		-
GO:0007186	G-protein coupled receptor protein signaling pathway	IEA		-
GO:0007368	determination of left/right symmetry	IEA		-
GO:0009953	dorsal/ventral pattern formation	IEA		-
GO:0048468	cell development	IEA		-
GO:0007389	pattern specification process	IEA		-
GO:0043066	negative regulation of apoptosis	IEA		-
GO:0042475	odontogenesis of dentine-containing tooth	IEA		-
GO:0021938	smoothened signaling pathway involved in regulation of granule cell precursor cell proliferation	IEA		-
GO:0043392	negative regulation of DNA binding	IEA		-
GO:0021696	cerebellar cortex morphogenesis	IEA		-
GO:0048589	developmental growth	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0016020	membrane	IEA		-
GO:0016021	integral to membrane	TAS		9422511
GO:0005929	cilium	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG HEDGEHOG SIGNALING PATHWAY	56	42	All SZGR 2.0 genes in this pathway
KEGG PATHWAYS IN CANCER	328	259	All SZGR 2.0 genes in this pathway
KEGG BASAL CELL CARCINOMA	55	44	All SZGR 2.0 genes in this pathway
BIOCARTA SHH PATHWAY	16	15	All SZGR 2.0 genes in this pathway
PID HEDGEHOG 2PATHWAY	22	17	All SZGR 2.0 genes in this pathway
PID HEDGEHOG GLI PATHWAY	48	35	All SZGR 2.0 genes in this pathway
REACTOME SIGNALING BY GPCR	920	449	All SZGR 2.0 genes in this pathway
REACTOME CLASS B 2 SECRETIN FAMILY RECEPTORS	88	58	All SZGR 2.0 genes in this pathway
REACTOME GPCR LIGAND BINDING	408	246	All SZGR 2.0 genes in this pathway
DOANE BREAST CANCER CLASSES DN	34	26	All SZGR 2.0 genes in this pathway
GROSS HYPOXIA VIA ELK3 UP	209	139	All SZGR 2.0 genes in this pathway
KOYAMA SEMA3B TARGETS DN	411	249	All SZGR 2.0 genes in this pathway
MATSUDA NATURAL KILLER DIFFERENTIATION	475	313	All SZGR 2.0 genes in this pathway
KUMAR TARGETS OF MLL AF9 FUSION	405	264	All SZGR 2.0 genes in this pathway
MURAKAMI UV RESPONSE 6HR DN	21	13	All SZGR 2.0 genes in this pathway
VERRECCHIA RESPONSE TO TGFB1 C5	21	11	All SZGR 2.0 genes in this pathway
VERRECCHIA DELAYED RESPONSE TO TGFB1	39	26	All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS STEM CELL AND PROGENITOR	681	420	All SZGR 2.0 genes in this pathway
MURAKAMI UV RESPONSE 24HR	20	13	All SZGR 2.0 genes in this pathway
GAVIN FOXP3 TARGETS CLUSTER T7	98	63	All SZGR 2.0 genes in this pathway
STEARMAN LUNG CANCER EARLY VS LATE UP	125	89	All SZGR 2.0 genes in this pathway
LEE METASTASIS AND ALTERNATIVE SPLICING UP	74	51	All SZGR 2.0 genes in this pathway
MARTINEZ RB1 TARGETS DN	543	317	All SZGR 2.0 genes in this pathway
MARTINEZ TP53 TARGETS DN	593	372	All SZGR 2.0 genes in this pathway
MARTINEZ RB1 AND TP53 TARGETS DN	591	366	All SZGR 2.0 genes in this pathway
BREDEMEYER RAG SIGNALING VIA ATM NOT VIA NFKB UP	49	32	All SZGR 2.0 genes in this pathway
YAUCH HEDGEHOG SIGNALING PARACRINE DN	264	159	All SZGR 2.0 genes in this pathway
GRESHOCK CANCER COPY NUMBER UP	323	240	All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K4ME3 AND H3K27ME3	1069	729	All SZGR 2.0 genes in this pathway
MURAKAMI UV RESPONSE 1HR DN	10	8	All SZGR 2.0 genes in this pathway
VERHAAK GLIOBLASTOMA CLASSICAL	162	122	All SZGR 2.0 genes in this pathway
PASINI SUZ12 TARGETS DN	315	215	All SZGR 2.0 genes in this pathway
TORCHIA TARGETS OF EWSR1 FLI1 FUSION TOP20 DN	18	12	All SZGR 2.0 genes in this pathway
TORCHIA TARGETS OF EWSR1 FLI1 FUSION DN	321	200	All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION UP	570	339	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-381	1086	1092	1A	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU

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: SMO