SZGR2

Summary ?

GeneID	7148
Symbol	TNXB
Synonyms	EDS3\|HXBL\|TENX\|TN-X\|TNX\|TNXB1\|TNXB2\|TNXBS\|VUR8\|XB\|XBS
Description	tenascin XB
Reference	MIM:600985\|HGNC:HGNC:11976\|Ensembl:ENSG00000168477\|HPRD:02993\|Vega:OTTHUMG00000031088
Gene type	protein-coding
Map location	6p21.3
Pascal p-value	1E-12
Sherlock p-value	0.287
Fetal beta	-0.668
DMG	1 (# studies)
eGene	Myers' cis & trans Meta

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).	7
PMID:cooccur	High-throughput literature-search	Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
Association	A combined odds ratio method (Sun et al. 2008), association studies	1	Link to SZGene
GSMA_I	Genome scan meta-analysis	Psr: 0.033
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophrenias	Click to show details

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg11493661	6	32016239	TNXB	9.05E-5	-0.463	0.027	DMG:Wockner_2014
cg26997880	6	32055370	TNXB	2.306E-4	-0.414	0.036	DMG:Wockner_2014
cg19071976	6	32026656	TNXB	2.489E-4	-0.717	0.037	DMG:Wockner_2014
cg18417373	6	32077097	TNXB	2.986E-4	-0.382	0.039	DMG:Wockner_2014
cg17001689	6	32055525	TNXB	3.289E-4	-0.592	0.041	DMG:Wockner_2014
cg09114581	6	32077103	TNXB	3.651E-4	-0.402	0.042	DMG:Wockner_2014
cg07481886	6	32014510	TNXB	4.761E-4	-0.303	0.046	DMG:Wockner_2014

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs2502827	chr1	176044216	TNXB	7148	0.1	trans
rs17572651	chr1	218943612	TNXB	7148	0.04	trans
rs16829545	chr2	151977407	TNXB	7148	4.646E-8	trans
rs3845734	chr2	171125572	TNXB	7148	0.03	trans
rs7584986	chr2	184111432	TNXB	7148	1.015E-4	trans
rs2322831	chr3	4799093	TNXB	7148	0.07	trans
rs7635430	chr3	180152035	TNXB	7148	0.16	trans
rs17762315	chr5	76807576	TNXB	7148	0.03	trans
rs7729096	chr5	76835927	TNXB	7148	0.02	trans
rs1368303	chr5	147672388	TNXB	7148	0.03	trans
rs13360496		0	TNXB	7148	0.17	trans
rs11139334	chr9	84209393	TNXB	7148	0.04	trans
rs3765543	chr9	134458323	TNXB	7148	0.07	trans
rs9506602	chr13	21638359	TNXB	7148	0.19	trans
rs17104720	chr14	77127308	TNXB	7148	0.07	trans
rs16955618	chr15	29937543	TNXB	7148	5.952E-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.

No co-expressed genes in brain regions

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005178	integrin binding	ISS		-
GO:0005518	collagen binding	IEA		-
GO:0008201	heparin binding	ISS		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007160	cell-matrix adhesion	IEA		-
GO:0007165	signal transduction	IEA		-
GO:0006641	triacylglycerol metabolic process	IEA		-
GO:0006631	fatty acid metabolic process	IEA		-
GO:0006629	lipid metabolic process	IEA		-
GO:0016337	cell-cell adhesion	IEA		-
GO:0030036	actin cytoskeleton organization	ISS		-
GO:0043506	regulation of JNK activity	IEA		-
GO:0030199	collagen fibril organization	IEA		-
GO:0048251	elastic fiber assembly	IMP		15102077
GO:0032963	collagen metabolic process	IMP		15102077
GO:0043206	fibril organization	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005576	extracellular region	IEA		-
GO:0005578	proteinaceous extracellular matrix	NAS		7686164
GO:0005583	fibrillar collagen	IDA		16278880
GO:0005615	extracellular space	IEA		-
GO:0005622	intracellular	IDA		15102077

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG FOCAL ADHESION	201	138	All SZGR 2.0 genes in this pathway
KEGG ECM RECEPTOR INTERACTION	84	53	All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA UP	1821	933	All SZGR 2.0 genes in this pathway
DELYS THYROID CANCER DN	232	154	All SZGR 2.0 genes in this pathway
CHIARADONNA NEOPLASTIC TRANSFORMATION KRAS DN	142	95	All SZGR 2.0 genes in this pathway
CHIARADONNA NEOPLASTIC TRANSFORMATION CDC25 DN	153	100	All SZGR 2.0 genes in this pathway
BERENJENO ROCK SIGNALING NOT VIA RHOA UP	29	21	All SZGR 2.0 genes in this pathway
VANHARANTA UTERINE FIBROID DN	67	45	All SZGR 2.0 genes in this pathway
ROPERO HDAC2 TARGETS	114	71	All SZGR 2.0 genes in this pathway
BERTUCCI INVASIVE CARCINOMA DUCTAL VS LOBULAR DN	46	34	All SZGR 2.0 genes in this pathway
SHEPARD BMYB MORPHOLINO DN	200	112	All SZGR 2.0 genes in this pathway
JECHLINGER EPITHELIAL TO MESENCHYMAL TRANSITION UP	71	51	All SZGR 2.0 genes in this pathway
SHEPARD BMYB TARGETS	74	41	All SZGR 2.0 genes in this pathway
SHEPARD CRUSH AND BURN MUTANT DN	185	111	All SZGR 2.0 genes in this pathway
YAO HOXA10 TARGETS VIA PROGESTERONE UP	79	58	All SZGR 2.0 genes in this pathway
NIELSEN LIPOSARCOMA UP	18	13	All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 3	101	64	All SZGR 2.0 genes in this pathway
TSENG IRS1 TARGETS DN	135	88	All SZGR 2.0 genes in this pathway
ZHONG SECRETOME OF LUNG CANCER AND ENDOTHELIUM	66	47	All SZGR 2.0 genes in this pathway
ZHONG SECRETOME OF LUNG CANCER AND FIBROBLAST	132	93	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER NORMAL LIKE UP	476	285	All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL UP	260	174	All SZGR 2.0 genes in this pathway
CHANG CORE SERUM RESPONSE DN	209	137	All SZGR 2.0 genes in this pathway
SWEET LUNG CANCER KRAS DN	435	289	All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3 UNMETHYLATED	536	296	All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K27ME3	269	159	All SZGR 2.0 genes in this pathway
BOYAULT LIVER CANCER SUBCLASS G3 DN	51	32	All SZGR 2.0 genes in this pathway
MIKKELSEN MEF HCP WITH H3K27ME3	590	403	All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 1	68	50	All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 2	86	50	All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS UP	745	475	All SZGR 2.0 genes in this pathway
FORTSCHEGGER PHF8 TARGETS DN	784	464	All SZGR 2.0 genes in this pathway
NABA ECM GLYCOPROTEINS	196	99	All SZGR 2.0 genes in this pathway
NABA CORE MATRISOME	275	148	All SZGR 2.0 genes in this pathway
NABA MATRISOME	1028	559	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-148/152	41	47	1A	hsa-miR-148a	UCAGUGCACUACAGAACUUUGU
				hsa-miR-152^brain	UCAGUGCAUGACAGAACUUGGG
				hsa-miR-148b	UCAGUGCAUCACAGAACUUUGU
miR-149	66	72	m8	hsa-miR-149^brain	UCUGGCUCCGUGUCUUCACUCC
miR-30-5p	132	139	1A,m8	hsa-miR-30a-5p	UGUAAACAUCCUCGACUGGAAG
				hsa-miR-30c^brain	UGUAAACAUCCUACACUCUCAGC
				hsa-miR-30d^SZ	UGUAAACAUCCCCGACUGGAAG
				hsa-miR-30b^SZ	UGUAAACAUCCUACACUCAGCU
				hsa-miR-30e-5p	UGUAAACAUCCUUGACUGGA
miR-423	37	43	1A	hsa-miR-423	AGCUCGGUCUGAGGCCCCUCAG

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: TNXB