SZGR2

Summary ?

GeneID	5166
Symbol	PDK4
Synonyms	-
Description	pyruvate dehydrogenase kinase 4
Reference	MIM:602527\|HGNC:HGNC:8812\|Ensembl:ENSG00000004799\|HPRD:03957\|Vega:OTTHUMG00000153977
Gene type	protein-coding
Map location	7q21.3
Pascal p-value	0.219
Sherlock p-value	0.277
DEG p-value	DEG:Zhao_2015:p=5.29e-05:q=0.0489
Fetal beta	-2.228
DMG	1 (# studies)
eGene	Cerebellar Hemisphere Myers' cis & trans

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
DEG:Zhao_2015	RNA Sequencing analysis	Transcriptome sequencing and genome-wide association analyses reveal lysosomal function and actin cytoskeleton remodeling in schizophrenia and bipolar disorder.
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).	1
Expression	Meta-analysis of gene expression	P value: 2.071

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg22171829	7	95225520	PDK4	1.843E-4	-0.625	0.034	DMG:Wockner_2014

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs1022180	chr6	165969395	PDK4	5166	0.11	trans
rs7032605	chr9	30426130	PDK4	5166	0.09	trans
rs10969802	chr9	30636427	PDK4	5166	0.03	trans
rs10969816	chr9	30661611	PDK4	5166	0.03	trans
rs12350524	chr9	30743421	PDK4	5166	0.03	trans
rs12343068	chr9	30783524	PDK4	5166	0.03	trans
rs10511868	chr9	30816504	PDK4	5166	0.03	trans
rs303549	chr9	106039392	PDK4	5166	0.12	trans
rs7334509	chr13	46692410	PDK4	5166	0.11	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
DNMT1	0.97	0.97
GCN1L1	0.96	0.96
NUP62	0.96	0.97
LIG3	0.96	0.96
ZXDC	0.95	0.95
BRPF1	0.95	0.96
SF1	0.95	0.97
GEMIN4	0.95	0.96
QRICH1	0.95	0.97
PRPF8	0.95	0.96

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AF347015.31	-0.78	-0.92
MT-CO2	-0.76	-0.92
AF347015.27	-0.75	-0.90
AF347015.33	-0.75	-0.88
C5orf53	-0.74	-0.79
FXYD1	-0.73	-0.87
MT-CYB	-0.73	-0.88
S100B	-0.73	-0.85
AF347015.8	-0.73	-0.90
HIGD1B	-0.72	-0.88

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0000155	two-component sensor activity	IEA		-
GO:0005524	ATP binding	IEA		-
GO:0004740	pyruvate dehydrogenase (acetyl-transferring) kinase activity	TAS		8798399
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0006006	glucose metabolic process	TAS		8798399
GO:0005975	carbohydrate metabolic process	IEA		-
GO:0007165	signal transduction	IEA		-
GO:0016310	phosphorylation	IEA		-
GO:0018106	peptidyl-histidine phosphorylation	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005739	mitochondrion	TAS		8798399
GO:0005743	mitochondrial inner membrane	IEA		-
GO:0005759	mitochondrial matrix	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
REACTOME PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE	48	32	All SZGR 2.0 genes in this pathway
REACTOME TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT	141	85	All SZGR 2.0 genes in this pathway
REACTOME REGULATION OF PYRUVATE DEHYDROGENASE PDH COMPLEX	13	9	All SZGR 2.0 genes in this pathway
REACTOME PYRUVATE METABOLISM	19	14	All SZGR 2.0 genes in this pathway
PARENT MTOR SIGNALING UP	567	375	All SZGR 2.0 genes in this pathway
LIU PROSTATE CANCER DN	481	290	All SZGR 2.0 genes in this pathway
SENGUPTA NASOPHARYNGEAL CARCINOMA WITH LMP1 DN	175	82	All SZGR 2.0 genes in this pathway
TURASHVILI BREAST LOBULAR CARCINOMA VS DUCTAL NORMAL DN	91	53	All SZGR 2.0 genes in this pathway
TURASHVILI BREAST LOBULAR CARCINOMA VS LOBULAR NORMAL UP	94	59	All SZGR 2.0 genes in this pathway
VECCHI GASTRIC CANCER EARLY DN	367	220	All SZGR 2.0 genes in this pathway
TAKEDA TARGETS OF NUP98 HOXA9 FUSION 8D DN	205	127	All SZGR 2.0 genes in this pathway
TAKEDA TARGETS OF NUP98 HOXA9 FUSION 10D DN	142	90	All SZGR 2.0 genes in this pathway
SENESE HDAC3 TARGETS UP	501	327	All SZGR 2.0 genes in this pathway
CHIARADONNA NEOPLASTIC TRANSFORMATION KRAS CDC25 DN	51	35	All SZGR 2.0 genes in this pathway
CHIARADONNA NEOPLASTIC TRANSFORMATION CDC25 UP	120	73	All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY SERUM DEPRIVATION UP	552	347	All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN UP	1142	669	All SZGR 2.0 genes in this pathway
GRAESSMANN RESPONSE TO MC AND DOXORUBICIN UP	612	367	All SZGR 2.0 genes in this pathway
BERENJENO TRANSFORMED BY RHOA DN	394	258	All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL BREAST 4 5WK DN	196	131	All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL BREAST 5 6WK UP	116	68	All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL TGFB1 TARGETS DN	62	44	All SZGR 2.0 genes in this pathway
SCHLOSSER SERUM RESPONSE DN	712	443	All SZGR 2.0 genes in this pathway
DAUER STAT3 TARGETS DN	50	34	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
RICKMAN HEAD AND NECK CANCER F	54	32	All SZGR 2.0 genes in this pathway
LIN SILENCED BY TUMOR MICROENVIRONMENT	108	73	All SZGR 2.0 genes in this pathway
NIKOLSKY BREAST CANCER 7Q21 Q22 AMPLICON	76	33	All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL AND BRAIN QTL TRANS	185	114	All SZGR 2.0 genes in this pathway
LEE LIVER CANCER CIPROFIBRATE UP	60	42	All SZGR 2.0 genes in this pathway
CHEN LVAD SUPPORT OF FAILING HEART UP	103	69	All SZGR 2.0 genes in this pathway
KAAB HEART ATRIUM VS VENTRICLE DN	261	183	All SZGR 2.0 genes in this pathway
SARTIPY BLUNTED BY INSULIN RESISTANCE DN	18	14	All SZGR 2.0 genes in this pathway
KAYO CALORIE RESTRICTION MUSCLE UP	95	64	All SZGR 2.0 genes in this pathway
MULLIGAN NTF3 SIGNALING VIA INSR AND IGF1R DN	13	6	All SZGR 2.0 genes in this pathway
MARTINEZ RB1 TARGETS UP	673	430	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 UP	601	369	All SZGR 2.0 genes in this pathway
WALLACE PROSTATE CANCER RACE UP	299	167	All SZGR 2.0 genes in this pathway
FUJII YBX1 TARGETS UP	43	28	All SZGR 2.0 genes in this pathway
RIGGI EWING SARCOMA PROGENITOR DN	191	123	All SZGR 2.0 genes in this pathway
BOCHKIS FOXA2 TARGETS	425	261	All SZGR 2.0 genes in this pathway
GRADE COLON AND RECTAL CANCER DN	101	65	All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL CULTURED VS FRESH UP	425	298	All SZGR 2.0 genes in this pathway
CADWELL ATG16L1 TARGETS DN	70	43	All SZGR 2.0 genes in this pathway
MOOTHA HUMAN MITODB 6 2002	429	260	All SZGR 2.0 genes in this pathway
MOOTHA PGC	420	269	All SZGR 2.0 genes in this pathway
MOOTHA MITOCHONDRIA	447	277	All SZGR 2.0 genes in this pathway
AGUIRRE PANCREATIC CANCER COPY NUMBER UP	298	174	All SZGR 2.0 genes in this pathway
CHIANG LIVER CANCER SUBCLASS CTNNB1 UP	176	110	All SZGR 2.0 genes in this pathway
CHIANG LIVER CANCER SUBCLASS PROLIFERATION DN	179	97	All SZGR 2.0 genes in this pathway
HOSHIDA LIVER CANCER SUBCLASS S3	266	180	All SZGR 2.0 genes in this pathway
UZONYI RESPONSE TO LEUKOTRIENE AND THROMBIN	37	26	All SZGR 2.0 genes in this pathway
NAKAYAMA SOFT TISSUE TUMORS PCA2 DN	80	51	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
HOELZEL NF1 TARGETS DN	115	73	All SZGR 2.0 genes in this pathway
OHGUCHI LIVER HNF4A TARGETS UP	44	30	All SZGR 2.0 genes in this pathway
BHAT ESR1 TARGETS NOT VIA AKT1 DN	88	61	All SZGR 2.0 genes in this pathway
BHAT ESR1 TARGETS VIA AKT1 DN	82	51	All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 3 UP	430	288	All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE LATE	1137	655	All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS UP	745	475	All SZGR 2.0 genes in this pathway
SERVITJA LIVER HNF1A TARGETS UP	135	96	All SZGR 2.0 genes in this pathway
PEDERSEN METASTASIS BY ERBB2 ISOFORM 6	29	20	All SZGR 2.0 genes in this pathway
WAKABAYASHI ADIPOGENESIS PPARG BOUND 8D	658	397	All SZGR 2.0 genes in this pathway
YANG BCL3 TARGETS UP	364	236	All SZGR 2.0 genes in this pathway
PLASARI TGFB1 TARGETS 10HR DN	244	157	All SZGR 2.0 genes in this pathway
PLASARI TGFB1 SIGNALING VIA NFIC 10HR UP	54	38	All SZGR 2.0 genes in this pathway
WANG MLL TARGETS	289	188	All SZGR 2.0 genes in this pathway
FORTSCHEGGER PHF8 TARGETS UP	279	155	All SZGR 2.0 genes in this pathway
PEDRIOLI MIR31 TARGETS DN	418	245	All SZGR 2.0 genes in this pathway
DURAND STROMA S UP	297	194	All SZGR 2.0 genes in this pathway
ZWANG DOWN BY 2ND EGF PULSE	293	119	All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 1ST EGF PULSE ONLY	1839	928	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	760	767	1A,m8	hsa-miR-148a	UCAGUGCACUACAGAACUUUGU
				hsa-miR-152^brain	UCAGUGCAUGACAGAACUUGGG
				hsa-miR-148b	UCAGUGCAUCACAGAACUUUGU
miR-15/16/195/424/497	49	55	m8	hsa-miR-15a^brain	UAGCAGCACAUAAUGGUUUGUG
				hsa-miR-16^brain	UAGCAGCACGUAAAUAUUGGCG
				hsa-miR-15b^brain	UAGCAGCACAUCAUGGUUUACA
				hsa-miR-195^SZ	UAGCAGCACAGAAAUAUUGGC
				hsa-miR-424	CAGCAGCAAUUCAUGUUUUGAA
				hsa-miR-497	CAGCAGCACACUGUGGUUUGU
miR-181	59	65	m8	hsa-miR-181a^brain	AACAUUCAACGCUGUCGGUGAGU
				hsa-miR-181b^SZ	AACAUUCAUUGCUGUCGGUGGG
				hsa-miR-181c^brain	AACAUUCAACCUGUCGGUGAGU
				hsa-miR-181d^brain	AACAUUCAUUGUUGUCGGUGGGUU
miR-9	1839	1846	1A,m8	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: PDK4