SZGR2

Summary ?

GeneID	7067
Symbol	THRA
Synonyms	AR7\|CHNG6\|EAR7\|ERB-T-1\|ERBA\|ERBA1\|NR1A1\|THRA1\|THRA2\|c-ERBA-1
Description	thyroid hormone receptor, alpha
Reference	MIM:190120\|HGNC:HGNC:11796\|Ensembl:ENSG00000126351\|HPRD:07185\|Vega:OTTHUMG00000133332
Gene type	protein-coding
Map location	17q11.2
Pascal p-value	0.042
Sherlock p-value	0.59
Fetal beta	-0.269
DMG	1 (# studies)
eGene	Myers' cis & trans
Support	CompositeSet Darnell FMRP targets

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,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
cg23121350	17	38219361	THRA	4.79E-8	-0.014	1.29E-5	DMG:Jaffe_2016

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs17542055	chr7	42652803	THRA	7067		0.15		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
UTP14C	0.96	0.97
MTDH	0.94	0.95
AC012621.2	0.94	0.95
TRIP12	0.94	0.95
PRKAA1	0.94	0.95
BCLAF1	0.93	0.95
GTF2A1	0.93	0.95
ZNF507	0.93	0.96
BAG5	0.93	0.94
CEP97	0.93	0.96

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AF347015.31	-0.72	-0.79
FXYD1	-0.71	-0.79
MT-CO2	-0.71	-0.80
HIGD1B	-0.69	-0.78
IFI27	-0.69	-0.78
ENHO	-0.68	-0.80
MT-CYB	-0.67	-0.75
AF347015.21	-0.67	-0.77
AF347015.8	-0.67	-0.76
AF347015.33	-0.67	-0.73

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
AKAP13	AKAP-Lbc \| BRX \| FLJ11952 \| FLJ43341 \| HA-3 \| Ht31 \| LBC \| PROTO-LB \| PROTO-LBC \| c-lbc	A kinase (PRKA) anchor protein 13	-	HPRD,BioGRID	9627117
BTG1	-	B-cell translocation gene 1, anti-proliferative	BTG1 interacts with THRA (TR-alpha-1). This interaction was modeled on a demonstrated interaction between human BTG1 and chicken or quail TR-alpha-1.	BIND	15674337
CCND1	BCL1 \| D11S287E \| PRAD1 \| U21B31	cyclin D1	-	HPRD,BioGRID	12048199
CDK7	CAK1 \| CDKN7 \| MO15 \| STK1 \| p39MO15	cyclin-dependent kinase 7	TR-alpha interacts with hMo15. This interaction was modeled on a demonstrated interaction between chicken TR-alpha and human hMo15.	BIND	15249124
CDK8	K35 \| MGC126074 \| MGC126075	cyclin-dependent kinase 8	Affinity Capture-Western	BioGRID	10198638
COPS2	ALIEN \| CSN2 \| SGN2 \| TRIP15	COP9 constitutive photomorphogenic homolog subunit 2 (Arabidopsis)	-	HPRD,BioGRID	10207062
CREB1	CREB \| MGC9284	cAMP responsive element binding protein 1	-	HPRD	12805224
DAP3	DAP-3 \| DKFZp686G12159 \| MGC126058 \| MGC126059 \| MRP-S29 \| MRPS29 \| bMRP-10	death associated protein 3	Reconstituted Complex	BioGRID	10903152
EP300	KAT3B \| p300	E1A binding protein p300	Affinity Capture-Western	BioGRID	12371907
FUS	CHOP \| FUS-CHOP \| FUS1 \| TLS \| TLS/CHOP \| hnRNP-P2	fusion (involved in t(12;16) in malignant liposarcoma)	-	HPRD,BioGRID	9440806
GTF2B	TF2B \| TFIIB	general transcription factor IIB	GTF2B (TFIIB) interacts with THRA (T3R-alpha). This interaction was modelled on a demonstrated interaction between human TFIIB and chicken T3R-alpha.	BIND	7609079
HDAC2	RPD3 \| YAF1	histone deacetylase 2	-	HPRD	10508171
HR	ALUNC \| AU \| HSA277165	hairless homolog (mouse)	Affinity Capture-Western	BioGRID	11641275
ITGB3BP	CENP-R \| CENPR \| HSU37139 \| NRIF3 \| TAP20	integrin beta 3 binding protein (beta3-endonexin)	Reconstituted Complex Two-hybrid	BioGRID	10490654 \|11713274
MED1	CRSP1 \| CRSP200 \| DRIP205 \| DRIP230 \| MGC71488 \| PBP \| PPARBP \| PPARGBP \| RB18A \| TRAP220 \| TRIP2	mediator complex subunit 1	-	HPRD,BioGRID	9653119
MED12	CAGH45 \| HOPA \| KIAA0192 \| OPA1 \| TNRC11 \| TRAP230	mediator complex subunit 12	Affinity Capture-MS Affinity Capture-Western	BioGRID	10198638
MED16	DRIP92 \| THRAP5 \| TRAP95	mediator complex subunit 16	Affinity Capture-MS Affinity Capture-Western	BioGRID	10198638
MED21	SRB7 \| SURB7	mediator complex subunit 21	TR-alpha interacts with hSrb7. This interaction was modeled on a demonstrated interaction between chicken TR-alpha and human hSrb7.	BIND	15249124
MED21	SRB7 \| SURB7	mediator complex subunit 21	Affinity Capture-Western	BioGRID	10198638
MED24	ARC100 \| CRSP100 \| CRSP4 \| DRIP100 \| KIAA0130 \| MGC8748 \| THRAP4 \| TRAP100	mediator complex subunit 24	Affinity Capture-Western	BioGRID	10198638
MED6	NY-REN-28	mediator complex subunit 6	Affinity Capture-MS Affinity Capture-Western	BioGRID	10198638
MEF2A	ADCAD1 \| RSRFC4 \| RSRFC9	myocyte enhancer factor 2A	-	HPRD,BioGRID	12371907
NCOA1	F-SRC-1 \| KAT13A \| MGC129719 \| MGC129720 \| NCoA-1 \| RIP160 \| SRC-1 \| SRC1 \| bHLHe42	nuclear receptor coactivator 1	TR-alpha interacts with SRC-1. This interaction was modeled on a demonstrated interaction between chicken TR-alpha and human SRC-1.	BIND	15249124
NCOA6	AIB3 \| ANTP \| ASC2 \| HOX1.1 \| HOXA7 \| KIAA0181 \| NRC \| PRIP \| RAP250 \| TRBP	nuclear receptor coactivator 6	Affinity Capture-Western Reconstituted Complex Two-hybrid	BioGRID	10567404 \|10847592 \|11158331
NR0B2	FLJ17090 \| SHP \| SHP1	nuclear receptor subfamily 0, group B, member 2	Reconstituted Complex	BioGRID	8650544
NR2F1	COUP-TFI \| EAR-3 \| EAR3 \| ERBAL3 \| NR2F2 \| SVP44 \| TCFCOUP1 \| TFCOUP1	nuclear receptor subfamily 2, group F, member 1	-	HPRD	1331778
NRIP1	FLJ77253 \| RIP140	nuclear receptor interacting protein 1	Reconstituted Complex	BioGRID	9626662
NSD1	ARA267 \| DKFZp666C163 \| FLJ10684 \| FLJ22263 \| FLJ44628 \| KMT3B \| SOTOS \| STO	nuclear receptor binding SET domain protein 1	-	HPRD	9628876
PARP1	ADPRT \| ADPRT1 \| PARP \| PARP-1 \| PPOL \| pADPRT-1	poly (ADP-ribose) polymerase 1	PARP-1 interacts with TR-alpha. This interaction was modeled on a demonstrated interaction between human PARP-1 and TR-alpha from an unspecified species.	BIND	15808511
PCSK2	NEC2 \| PC2 \| SPC2	proprotein convertase subtilisin/kexin type 2	THRA interacts with the PCSK2 (PC2) promoter. This interaction was modelled on a demonstrated interaction between chicken THRA and human PCSK2 (PC2) promoter.	BIND	10965896
PML	MYL \| PP8675 \| RNF71 \| TRIM19	promyelocytic leukemia	-	HPRD	10610177
POU2F1	OCT1 \| OTF1	POU class 2 homeobox 1	Reconstituted Complex	BioGRID	10480874
RXRA	FLJ00280 \| FLJ00318 \| FLJ16020 \| FLJ16733 \| MGC102720 \| NR2B1	retinoid X receptor, alpha	Co-purification	BioGRID	1314167
RXRA	FLJ00280 \| FLJ00318 \| FLJ16020 \| FLJ16733 \| MGC102720 \| NR2B1	retinoid X receptor, alpha	-	HPRD	1331778
RXRB	DAUDI6 \| H-2RIIBP \| MGC1831 \| NR2B2 \| RCoR-1	retinoid X receptor, beta	-	HPRD	1331778
TDG	-	thymine-DNA glycosylase	-	HPRD,BioGRID	12874288
TRIM24	PTC6 \| RNF82 \| TF1A \| TIF1 \| TIF1A \| TIF1ALPHA \| hTIF1	tripartite motif-containing 24	Reconstituted Complex	BioGRID	9115274
TRIP11	CEV14 \| GMAP-210 \| TRIP230	thyroid hormone receptor interactor 11	Affinity Capture-Western Reconstituted Complex	BioGRID	9256431
YWHAH	YWHA1	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide	-	HPRD	11266503
YWHAQ	14-3-3 \| 1C5 \| HS1	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide	Reconstituted Complex	BioGRID	11266503

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION	272	195	All SZGR 2.0 genes in this pathway
BIOCARTA EGFR SMRTE PATHWAY	11	11	All SZGR 2.0 genes in this pathway
PID RXR VDR PATHWAY	26	24	All SZGR 2.0 genes in this pathway
REACTOME GENERIC TRANSCRIPTION PATHWAY	352	181	All SZGR 2.0 genes in this pathway
REACTOME NUCLEAR RECEPTOR TRANSCRIPTION PATHWAY	49	36	All SZGR 2.0 genes in this pathway
GAZDA DIAMOND BLACKFAN ANEMIA ERYTHROID DN	493	298	All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA UP	1821	933	All SZGR 2.0 genes in this pathway
CHIN BREAST CANCER COPY NUMBER UP	27	18	All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN DN	1781	1082	All SZGR 2.0 genes in this pathway
BERENJENO TRANSFORMED BY RHOA DN	394	258	All SZGR 2.0 genes in this pathway
SCHLOSSER SERUM RESPONSE DN	712	443	All SZGR 2.0 genes in this pathway
DAIRKEE TERT TARGETS UP	380	213	All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK	1442	892	All SZGR 2.0 genes in this pathway
LOPEZ MBD TARGETS	957	597	All SZGR 2.0 genes in this pathway
LIU LIVER CANCER	38	18	All SZGR 2.0 genes in this pathway
NIKOLSKY BREAST CANCER 17Q11 Q21 AMPLICON	133	78	All SZGR 2.0 genes in this pathway
FERNANDEZ BOUND BY MYC	182	116	All SZGR 2.0 genes in this pathway
JOSEPH RESPONSE TO SODIUM BUTYRATE DN	64	45	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP	1691	1088	All SZGR 2.0 genes in this pathway
TSENG IRS1 TARGETS DN	135	88	All SZGR 2.0 genes in this pathway
DEBIASI APOPTOSIS BY REOVIRUS INFECTION DN	287	208	All SZGR 2.0 genes in this pathway
SANSOM APC MYC TARGETS	217	138	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
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
BHATI G2M ARREST BY 2METHOXYESTRADIOL DN	127	75	All SZGR 2.0 genes in this pathway
HOFFMANN PRE BI TO LARGE PRE BII LYMPHOCYTE DN	75	61	All SZGR 2.0 genes in this pathway
ZHANG TLX TARGETS 60HR UP	293	203	All SZGR 2.0 genes in this pathway
SHEDDEN LUNG CANCER GOOD SURVIVAL A12	317	177	All SZGR 2.0 genes in this pathway
DANG REGULATED BY MYC UP	72	53	All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS UP	745	475	All SZGR 2.0 genes in this pathway

Gene Page: THRA