SZGR2

Summary ?

GeneID	10891
Symbol	PPARGC1A
Synonyms	LEM6\|PGC-1(alpha)\|PGC-1alpha\|PGC-1v\|PGC1\|PGC1A\|PPARGC1
Description	PPARG coactivator 1 alpha
Reference	MIM:604517\|HGNC:HGNC:9237\|Ensembl:ENSG00000109819\|HPRD:05155\|Vega:OTTHUMG00000097747
Gene type	protein-coding
Map location	4p15.1
Pascal p-value	0.011
Sherlock p-value	0.004
Fetal beta	-2.1
DMG	1 (# studies)
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,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
cg08811082	4	24474861	PPARGC1A	4.48E-8	-0.007	1.23E-5	DMG:Jaffe_2016

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:0000166	nucleotide binding	IEA		-
GO:0003677	DNA binding	TAS		10713165
GO:0003723	RNA binding	TAS		12588810
GO:0008134	transcription factor binding	TAS		12588810
GO:0016455	RNA polymerase II transcription mediator activity	TAS		14636573
GO:0030374	ligand-dependent nuclear receptor transcription coactivator activity	TAS		12588810
GO:0050681	androgen receptor binding	NAS		15572661
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0001659	temperature homeostasis	TAS		1258810
GO:0001678	cellular glucose homeostasis	NAS		11854298
GO:0006367	transcription initiation from RNA polymerase II promoter	TAS		14636573
GO:0006397	mRNA processing	TAS		12588810
GO:0008380	RNA splicing	TAS		12588810
GO:0006461	protein complex assembly	TAS		14636573
GO:0007586	digestion	TAS		10585775
GO:0007005	mitochondrion organization	NAS		11854298
GO:0042594	response to starvation	NAS		11854298
GO:0050821	protein stabilization	TAS		14636573
GO:0050873	brown fat cell differentiation	TAS		12588810
GO:0035066	positive regulation of histone acetylation	TAS		14636573
GO:0030521	androgen receptor signaling pathway	NAS		15572661
GO:0045333	cellular respiration	TAS		11551810
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	IEA		-
GO:0045722	positive regulation of gluconeogenesis	TAS		12588810
GO:0046321	positive regulation of fatty acid oxidation	TAS		12588810
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005634	nucleus	TAS		12588810
GO:0005665	DNA-directed RNA polymerase II, core complex	TAS		12588810

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
ESR1	DKFZp686N23123 \| ER \| ESR \| ESRA \| Era \| NR3A1	estrogen receptor 1	-	HPRD,BioGRID	10748020
ESRRG	DKFZp781L1617 \| ERR3 \| FLJ16023 \| KIAA0832 \| NR3B3	estrogen-related receptor gamma	-	HPRD,BioGRID	12470660
HCFC1	CFF \| HCF-1 \| HCF1 \| HFC1 \| MGC70925 \| VCAF	host cell factor C1 (VP16-accessory protein)	-	HPRD,BioGRID	11733490
MED1	CRSP1 \| CRSP200 \| DRIP205 \| DRIP230 \| MGC71488 \| PBP \| PPARBP \| PPARGBP \| RB18A \| TRAP220 \| TRIP2	mediator complex subunit 1	-	HPRD,BioGRID	14636573
MED12	CAGH45 \| HOPA \| KIAA0192 \| OPA1 \| TNRC11 \| TRAP230	mediator complex subunit 12	Affinity Capture-Western Reconstituted Complex	BioGRID	14636573
MED14	CRSP150 \| CRSP2 \| CSRP \| CXorf4 \| DRIP150 \| EXLM1 \| MGC104513 \| RGR1 \| TRAP170	mediator complex subunit 14	Affinity Capture-Western Reconstituted Complex	BioGRID	14636573
MED16	DRIP92 \| THRAP5 \| TRAP95	mediator complex subunit 16	Affinity Capture-Western	BioGRID	14636573
MED17	CRSP6 \| CRSP77 \| DRIP80 \| FLJ10812 \| TRAP80	mediator complex subunit 17	Affinity Capture-Western Reconstituted Complex	BioGRID	14636573
MED20	DKFZp586D2223 \| MGC29869 \| PRO0213 \| TRFP	mediator complex subunit 20	Affinity Capture-Western	BioGRID	14636573
MED21	SRB7 \| SURB7	mediator complex subunit 21	Affinity Capture-Western	BioGRID	14636573
NCL	C23 \| FLJ45706	nucleolin	-	HPRD	10983978
NCOA1	F-SRC-1 \| KAT13A \| MGC129719 \| MGC129720 \| NCoA-1 \| RIP160 \| SRC-1 \| SRC1 \| bHLHe42	nuclear receptor coactivator 1	-	HPRD,BioGRID	10558993
NR1H4	BAR \| FXR \| HRR-1 \| HRR1 \| MGC163445 \| RIP14	nuclear receptor subfamily 1, group H, member 4	-	HPRD,BioGRID	14729567
NR1I3	CAR \| CAR1 \| MB67 \| MGC150433 \| MGC97144 \| MGC97209	nuclear receptor subfamily 1, group I, member 3	CAR interacts with PGC-1.	BIND	15572376
NR3C1	GCCR \| GCR \| GR \| GRL	nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)	-	HPRD,BioGRID	10713165
NRF1	ALPHA-PAL	nuclear respiratory factor 1	-	HPRD,BioGRID	10412986 \|11943463
PPARA	MGC2237 \| MGC2452 \| NR1C1 \| PPAR \| hPPAR	peroxisome proliferator-activated receptor alpha	-	HPRD,BioGRID	10669761
PPARG	NR1C3 \| PPARG1 \| PPARG2 \| PPARgamma	peroxisome proliferator-activated receptor gamma	-	HPRD	12502716
PPARG	NR1C3 \| PPARG1 \| PPARG2 \| PPARgamma	peroxisome proliferator-activated receptor gamma	Reconstituted Complex	BioGRID	14636573
RXRA	FLJ00280 \| FLJ00318 \| FLJ16020 \| FLJ16733 \| MGC102720 \| NR2B1	retinoid X receptor, alpha	-	HPRD,BioGRID	11714715
SFRS2	PR264 \| SC-35 \| SC35 \| SFRS2A \| SRp30b	splicing factor, arginine/serine-rich 2	Affinity Capture-Western	BioGRID	10983978
SFRS4	SRP75	splicing factor, arginine/serine-rich 4	Affinity Capture-Western	BioGRID	10983978
SFRS5	HRS \| SRP40	splicing factor, arginine/serine-rich 5	Affinity Capture-Western	BioGRID	10983978
SFRS6	B52 \| FLJ08061 \| MGC5045 \| SRP55	splicing factor, arginine/serine-rich 6	Affinity Capture-Western	BioGRID	10983978
THRB	ERBA-BETA \| ERBA2 \| GRTH \| MGC126109 \| MGC126110 \| NR1A2 \| PRTH \| THR1 \| THRB1 \| THRB2	thyroid hormone receptor, beta (erythroblastic leukemia viral (v-erb-a) oncogene homolog 2, avian)	-	HPRD,BioGRID	11751919
USF2	FIP \| bHLHb12	upstream transcription factor 2, c-fos interacting	-	HPRD	12611894

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG INSULIN SIGNALING PATHWAY	137	103	All SZGR 2.0 genes in this pathway
KEGG ADIPOCYTOKINE SIGNALING PATHWAY	67	57	All SZGR 2.0 genes in this pathway
KEGG HUNTINGTONS DISEASE	185	109	All SZGR 2.0 genes in this pathway
BIOCARTA CARM ER PATHWAY	35	27	All SZGR 2.0 genes in this pathway
BIOCARTA PPARA PATHWAY	58	43	All SZGR 2.0 genes in this pathway
BIOCARTA PGC1A PATHWAY	26	20	All SZGR 2.0 genes in this pathway
PID HDAC CLASSIII PATHWAY	25	20	All SZGR 2.0 genes in this pathway
PID MTOR 4PATHWAY	69	55	All SZGR 2.0 genes in this pathway
PID ATF2 PATHWAY	59	43	All SZGR 2.0 genes in this pathway
PID P38 ALPHA BETA DOWNSTREAM PATHWAY	38	29	All SZGR 2.0 genes in this pathway
REACTOME DEVELOPMENTAL BIOLOGY	396	292	All SZGR 2.0 genes in this pathway
REACTOME BMAL1 CLOCK NPAS2 ACTIVATES CIRCADIAN EXPRESSION	36	27	All SZGR 2.0 genes in this pathway
REACTOME PPARA ACTIVATES GENE EXPRESSION	104	72	All SZGR 2.0 genes in this pathway
REACTOME RORA ACTIVATES CIRCADIAN EXPRESSION	24	17	All SZGR 2.0 genes in this pathway
REACTOME CIRCADIAN REPRESSION OF EXPRESSION BY REV ERBA	23	16	All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF LIPIDS AND LIPOPROTEINS	478	302	All SZGR 2.0 genes in this pathway
REACTOME FATTY ACID TRIACYLGLYCEROL AND KETONE BODY METABOLISM	168	115	All SZGR 2.0 genes in this pathway
REACTOME CIRCADIAN CLOCK	53	40	All SZGR 2.0 genes in this pathway
REACTOME TRANSCRIPTIONAL REGULATION OF WHITE ADIPOCYTE DIFFERENTIATION	72	53	All SZGR 2.0 genes in this pathway
MULLIGHAN NPM1 MUTATED SIGNATURE 1 UP	276	165	All SZGR 2.0 genes in this pathway
MULLIGHAN NPM1 MUTATED SIGNATURE 2 UP	139	83	All SZGR 2.0 genes in this pathway
MULLIGHAN NPM1 SIGNATURE 3 UP	341	197	All SZGR 2.0 genes in this pathway
HAMAI APOPTOSIS VIA TRAIL UP	584	356	All SZGR 2.0 genes in this pathway
MATSUDA NATURAL KILLER DIFFERENTIATION	475	313	All SZGR 2.0 genes in this pathway
HELLER SILENCED BY METHYLATION DN	105	67	All SZGR 2.0 genes in this pathway
WALLACE PROSTATE CANCER RACE UP	299	167	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER DN	540	340	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE DN	274	165	All SZGR 2.0 genes in this pathway
MITSIADES RESPONSE TO APLIDIN UP	439	257	All SZGR 2.0 genes in this pathway
CADWELL ATG16L1 TARGETS DN	70	43	All SZGR 2.0 genes in this pathway
YAMASHITA LIVER CANCER STEM CELL DN	76	51	All SZGR 2.0 genes in this pathway
BOYLAN MULTIPLE MYELOMA PCA3 UP	80	54	All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA DN	267	160	All SZGR 2.0 genes in this pathway
MIKKELSEN NPC ICP WITH H3K4ME3	445	257	All SZGR 2.0 genes in this pathway
YANG BCL3 TARGETS UP	364	236	All SZGR 2.0 genes in this pathway
GUO TARGETS OF IRS1 AND IRS2	98	67	All SZGR 2.0 genes in this pathway
ACEVEDO FGFR1 TARGETS IN PROSTATE CANCER MODEL UP	289	184	All SZGR 2.0 genes in this pathway
CHEMELLO SOLEUS VS EDL MYOFIBERS UP	35	16	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
let-7/98	38	44	1A	hsa-let-7a^brain	UGAGGUAGUAGGUUGUAUAGUU
				hsa-let-7b^brain	UGAGGUAGUAGGUUGUGUGGUU
				hsa-let-7c^brain	UGAGGUAGUAGGUUGUAUGGUU
				hsa-let-7d^brain	AGAGGUAGUAGGUUGCAUAGU
				hsa-let-7e^brain	UGAGGUAGGAGGUUGUAUAGU
				hsa-let-7f^brain	UGAGGUAGUAGAUUGUAUAGUU
				hsa-miR-98^brain	UGAGGUAGUAAGUUGUAUUGUU
				hsa-let-7g^SZ	UGAGGUAGUAGUUUGUACAGU
				hsa-let-7i^brain	UGAGGUAGUAGUUUGUGCUGU
miR-136	1092	1098	m8	hsa-miR-136	ACUCCAUUUGUUUUGAUGAUGGA
miR-137	2656	2662	1A	hsa-miR-137	UAUUGCUUAAGAAUACGCGUAG
miR-137	2656	2662	1A	hsa-miR-137	UAUUGCUUAAGAAUACGCGUAG
miR-138	2360	2367	1A,m8	hsa-miR-138^brain	AGCUGGUGUUGUGAAUC
miR-139	3453	3459	m8	hsa-miR-139^brain	UCUACAGUGCACGUGUCU
miR-148/152	1152	1158	m8	hsa-miR-148a	UCAGUGCACUACAGAACUUUGU
				hsa-miR-152^brain	UCAGUGCAUGACAGAACUUGGG
				hsa-miR-148b	UCAGUGCAUCACAGAACUUUGU
miR-150	805	811	1A	hsa-miR-150	UCUCCCAACCCUUGUACCAGUG
miR-153	1149	1155	m8	hsa-miR-153	UUGCAUAGUCACAAAAGUGA
miR-193	1754	1760	1A	hsa-miR-193a	AACUGGCCUACAAAGUCCCAG
miR-193	1754	1760	1A	hsa-miR-193b	AACUGGCCCUCAAAGUCCCGCUUU
miR-194	1141	1147	1A	hsa-miR-194	UGUAACAGCAACUCCAUGUGGA
miR-199	1485	1492	1A,m8	hsa-miR-199a	CCCAGUGUUCAGACUACCUGUUC
miR-199	1485	1492	1A,m8	hsa-miR-199b	CCCAGUGUUUAGACUAUCUGUUC
miR-204/211	3776	3783	1A,m8	hsa-miR-204^brain	UUCCCUUUGUCAUCCUAUGCCU
miR-204/211	3776	3783	1A,m8	hsa-miR-211	UUCCCUUUGUCAUCCUUCGCCU
miR-214	194	200	1A	hsa-miR-214^brain	ACAGCAGGCACAGACAGGCAG
miR-217	3746	3752	1A	hsa-miR-217	UACUGCAUCAGGAACUGAUUGGAU
miR-218	229	235	m8	hsa-miR-218^brain	UUGUGCUUGAUCUAACCAUGU
miR-219	698	704	m8	hsa-miR-219^brain	UGAUUGUCCAAACGCAAUUCU
miR-22	2329	2335	1A	hsa-miR-22^brain	AAGCUGCCAGUUGAAGAACUGU
miR-221/222	3222	3229	1A,m8	hsa-miR-221^brain	AGCUACAUUGUCUGCUGGGUUUC
miR-221/222	3222	3229	1A,m8	hsa-miR-222^brain	AGCUACAUCUGGCUACUGGGUCUC
miR-23	3504	3510	m8	hsa-miR-23a^brain	AUCACAUUGCCAGGGAUUUCC
				hsa-miR-23b^brain	AUCACAUUGCCAGGGAUUACC
				hsa-miR-23a^brain	AUCACAUUGCCAGGGAUUUCC
				hsa-miR-23b^brain	AUCACAUUGCCAGGGAUUACC
miR-29	3181	3187	m8	hsa-miR-29a^SZ	UAGCACCAUCUGAAAUCGGUU
				hsa-miR-29b^SZ	UAGCACCAUUUGAAAUCAGUGUU
				hsa-miR-29c^SZ	UAGCACCAUUUGAAAUCGGU
miR-30-5p	1850	1856	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
				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
				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-320	253	259	m8	hsa-miR-320	AAAAGCUGGGUUGAGAGGGCGAA
miR-323	3549	3556	1A,m8	hsa-miR-323^brain	GCACAUUACACGGUCGACCUCU
miR-323	3549	3556	1A,m8	hsa-miR-323^brain	GCACAUUACACGGUCGACCUCU
miR-33	2325	2331	m8	hsa-miR-33	GUGCAUUGUAGUUGCAUUG
miR-33	2325	2331	m8	hsa-miR-33b	GUGCAUUGCUGUUGCAUUGCA
miR-369-3p	1893	1899	1A	hsa-miR-369-3p	AAUAAUACAUGGUUGAUCUUU
miR-374	1893	1900	1A,m8	hsa-miR-374	UUAUAAUACAACCUGAUAAGUG
miR-410	1275	1281	1A	hsa-miR-410	AAUAUAACACAGAUGGCCUGU
miR-433-3p	1540	1546	m8	hsa-miR-433^brain	AUCAUGAUGGGCUCCUCGGUGU
miR-485-3p	3714	3721	1A,m8	hsa-miR-485-3p	GUCAUACACGGCUCUCCUCUCU
miR-485-5p	3758	3765	1A,m8	hsa-miR-485-5p	AGAGGCUGGCCGUGAUGAAUUC
miR-494	3788	3795	1A,m8	hsa-miR-494^brain	UGAAACAUACACGGGAAACCUCUU
miR-495	1139	1145	1A	hsa-miR-495^brain	AAACAAACAUGGUGCACUUCUUU
miR-495	1139	1145	1A	hsa-miR-495^brain	AAACAAACAUGGUGCACUUCUUU
miR-496	1551	1557	1A	hsa-miR-496	AUUACAUGGCCAAUCUC
miR-539	93	99	m8	hsa-miR-539	GGAGAAAUUAUCCUUGGUGUGU
miR-539	93	99	m8	hsa-miR-539	GGAGAAAUUAUCCUUGGUGUGU
miR-543	3786	3792	m8	hsa-miR-543	AAACAUUCGCGGUGCACUUCU
miR-7	911	917	1A	hsa-miR-7^SZ	UGGAAGACUAGUGAUUUUGUUG

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: PPARGC1A