SZGR2

Summary ?

GeneID	4800
Symbol	NFYA
Synonyms	CBF-A\|CBF-B\|HAP2\|NF-YA
Description	nuclear transcription factor Y subunit alpha
Reference	MIM:189903\|HGNC:HGNC:7804\|HPRD:01793\|
Gene type	protein-coding
Map location	6p21.3
Pascal p-value	0.497
Fetal beta	1.563
DMG	1 (# studies)
eGene	Cerebellum

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:GWASdb	Genome-wide Association Studies	GWASdb records for schizophrenia
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
GSMA_I	Genome scan meta-analysis	Psr: 0.033
GSMA_IIE	Genome scan meta-analysis (European-ancestry samples)	Psr: 0.04433

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg12694820	6	41041189	NFYA	1.6E-8	-0.01	5.94E-6	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.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
NME1-NME2	0.98	0.98
C2orf79	0.89	0.91
MYL6	0.89	0.89
NME2P1	0.89	0.84
RPL12	0.89	0.83
COMMD6	0.86	0.84
RPL36	0.86	0.81
TCTEX1D2	0.85	0.84
RP11-544M22.1	0.85	0.83
UFC1	0.85	0.85

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
MYH14	-0.53	-0.65
AF347015.26	-0.53	-0.65
AF347015.33	-0.51	-0.61
EPAS1	-0.51	-0.61
KIF1C	-0.51	-0.65
ZBTB7B	-0.51	-0.62
AF347015.15	-0.51	-0.60
AF347015.27	-0.50	-0.59
FYCO1	-0.50	-0.61
AF347015.8	-0.50	-0.58

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0003700	transcription factor activity	TAS		1774067 \|2000400
GO:0005515	protein binding	IPI		10571058 \|12659632 \|12741956
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0006355	regulation of transcription, DNA-dependent	IDA		15243141
GO:0006350	transcription	IEA		-
GO:0006366	transcription from RNA polymerase II promoter	TAS		2000400
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005634	nucleus	IDA		15243141
GO:0016602	CCAAT-binding factor complex	IDA		15243141

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
APPBP2	HS.84084 \| KIAA0228 \| PAT1	amyloid beta precursor protein (cytoplasmic tail) binding protein 2	Two-hybrid	BioGRID	16189514
ATF6	ATF6A	activating transcription factor 6	Two-hybrid	BioGRID	11158310
ATF6B	CREB-RP \| CREBL1 \| FLJ10066 \| G13	activating transcription factor 6 beta	Two-hybrid	BioGRID	11158310
BRCA1	BRCAI \| BRCC1 \| IRIS \| PSCP \| RNF53	breast cancer 1, early onset	-	HPRD,BioGRID	11777930
BRCA1	BRCAI \| BRCC1 \| IRIS \| PSCP \| RNF53	breast cancer 1, early onset	BRCA1 interacts with NF-YA	BIND	11777930
ELF1	-	E74-like factor 1 (ets domain transcription factor)	Reconstituted Complex	BioGRID	9668064
HMGA1	HMG-R \| HMGA1A \| HMGIY \| MGC12816 \| MGC4242 \| MGC4854	high mobility group AT-hook 1	-	HPRD,BioGRID	9388234
JUN	AP-1 \| AP1 \| c-Jun	jun oncogene	Affinity Capture-Western	BioGRID	11903046
NFYB	CBF-A \| CBF-B \| HAP3 \| NF-YB	nuclear transcription factor Y, beta	-	HPRD,BioGRID	8051128
POU2F1	OCT1 \| OTF1	POU class 2 homeobox 1	-	HPRD	11777930
POU2F1	OCT1 \| OTF1	POU class 2 homeobox 1	Oct-1 interacts with NF-YA	BIND	11777930
SPI1	OF \| PU.1 \| SFPI1 \| SPI-1 \| SPI-A	spleen focus forming virus (SFFV) proviral integration oncogene spi1	Reconstituted Complex	BioGRID	9668064
SRF	MCM1	serum response factor (c-fos serum response element-binding transcription factor)	NF-YA interacts with SRF. This interaction was modeled on a demonstrated interaction between NF-YA from an unspecified species and SRF from human.	BIND	10571058
SRF	MCM1	serum response factor (c-fos serum response element-binding transcription factor)	Reconstituted Complex Two-hybrid	BioGRID	10571058
ZHX1	-	zinc fingers and homeoboxes 1	NF-YA interacts with ZHX1. This interaction was modeled on a demonstrated interaction between NF-YA from an unspecified species and ZHX1 from human.	BIND	10571058
ZHX1	-	zinc fingers and homeoboxes 1	-	HPRD,BioGRID	10441475 \|10571058
ZHX2	AFR1 \| KIAA0854 \| RAF	zinc fingers and homeoboxes 2	-	HPRD	12741956
ZHX3	KIAA0395 \| TIX1	zinc fingers and homeoboxes 3	-	HPRD	12659632

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG ANTIGEN PROCESSING AND PRESENTATION	89	65	All SZGR 2.0 genes in this pathway
PID P53 DOWNSTREAM PATHWAY	137	94	All SZGR 2.0 genes in this pathway
PID MYC REPRESS PATHWAY	63	52	All SZGR 2.0 genes in this pathway
REACTOME PPARA ACTIVATES GENE EXPRESSION	104	72	All SZGR 2.0 genes in this pathway
REACTOME DIABETES PATHWAYS	133	91	All SZGR 2.0 genes in this pathway
REACTOME PERK REGULATED GENE EXPRESSION	29	14	All SZGR 2.0 genes in this pathway
REACTOME ACTIVATION OF CHAPERONES BY ATF6 ALPHA	13	9	All SZGR 2.0 genes in this pathway
REACTOME ACTIVATION OF GENES BY ATF4	26	12	All SZGR 2.0 genes in this pathway
REACTOME UNFOLDED PROTEIN RESPONSE	80	51	All SZGR 2.0 genes in this pathway
REACTOME ACTIVATION OF CHAPERONE GENES BY ATF6 ALPHA	11	8	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
GAZDA DIAMOND BLACKFAN ANEMIA ERYTHROID DN	493	298	All SZGR 2.0 genes in this pathway
PUIFFE INVASION INHIBITED BY ASCITES DN	145	91	All SZGR 2.0 genes in this pathway
CASORELLI ACUTE PROMYELOCYTIC LEUKEMIA UP	177	110	All SZGR 2.0 genes in this pathway
OSMAN BLADDER CANCER DN	406	230	All SZGR 2.0 genes in this pathway
GARGALOVIC RESPONSE TO OXIDIZED PHOSPHOLIPIDS GREEN DN	25	12	All SZGR 2.0 genes in this pathway
SENESE HDAC1 TARGETS UP	457	269	All SZGR 2.0 genes in this pathway
SENESE HDAC3 TARGETS UP	501	327	All SZGR 2.0 genes in this pathway
KINSEY TARGETS OF EWSR1 FLII FUSION UP	1278	748	All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS 8HR DN	129	84	All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN DN	1781	1082	All SZGR 2.0 genes in this pathway
TANAKA METHYLATED IN ESOPHAGEAL CARCINOMA	103	58	All SZGR 2.0 genes in this pathway
PATIL LIVER CANCER	747	453	All SZGR 2.0 genes in this pathway
PUJANA BRCA2 PCC NETWORK	423	265	All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS DN	1024	594	All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS UP	811	508	All SZGR 2.0 genes in this pathway
RICKMAN TUMOR DIFFERENTIATED WELL VS POORLY UP	236	139	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 6HR DN	514	330	All SZGR 2.0 genes in this pathway
GEORGES CELL CYCLE MIR192 TARGETS	62	46	All SZGR 2.0 genes in this pathway
GEORGES TARGETS OF MIR192 AND MIR215	893	528	All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL QTL CIS	128	77	All SZGR 2.0 genes in this pathway
FLECHNER PBL KIDNEY TRANSPLANT OK VS DONOR DN	41	30	All SZGR 2.0 genes in this pathway
FLECHNER PBL KIDNEY TRANSPLANT REJECTED VS OK UP	63	48	All SZGR 2.0 genes in this pathway
ADDYA ERYTHROID DIFFERENTIATION BY HEMIN	73	47	All SZGR 2.0 genes in this pathway
KANG FLUOROURACIL RESISTANCE DN	16	10	All SZGR 2.0 genes in this pathway
XU GH1 EXOGENOUS TARGETS UP	85	50	All SZGR 2.0 genes in this pathway
LEE AGING CEREBELLUM UP	84	58	All SZGR 2.0 genes in this pathway
DOUGLAS BMI1 TARGETS UP	566	371	All SZGR 2.0 genes in this pathway
MARSON BOUND BY E2F4 UNSTIMULATED	728	415	All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS SILENCED BY METHYLATION UP	461	298	All SZGR 2.0 genes in this pathway
AMUNDSON POOR SURVIVAL AFTER GAMMA RADIATION 2G	171	96	All SZGR 2.0 genes in this pathway
BOYLAN MULTIPLE MYELOMA C CLUSTER UP	38	26	All SZGR 2.0 genes in this pathway
BOYLAN MULTIPLE MYELOMA C UP	47	29	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 30MIN DN	150	99	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 4HR DN	254	158	All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN	1972	1213	All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 2 DN	336	211	All SZGR 2.0 genes in this pathway
JUBAN TARGETS OF SPI1 AND FLI1 DN	92	60	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-132/212	221	227	m8	hsa-miR-212^SZ	UAACAGUCUCCAGUCACGGCC
miR-132/212	221	227	m8	hsa-miR-132^brain	UAACAGUCUACAGCCAUGGUCG
miR-200bc/429	142	149	1A,m8	hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
miR-22	1274	1280	m8	hsa-miR-22^brain	AAGCUGCCAGUUGAAGAACUGU
miR-330	686	692	1A	hsa-miR-330^brain	GCAAAGCACACGGCCUGCAGAGA
miR-504	1390	1397	1A,m8	hsa-miR-504	AGACCCUGGUCUGCACUCUAU
miR-93.hd/291-3p/294/295/302/372/373/520	294	301	1A,m8	hsa-miR-93^brain	AAAGUGCUGUUCGUGCAGGUAG
				hsa-miR-302a	UAAGUGCUUCCAUGUUUUGGUGA
				hsa-miR-302b	UAAGUGCUUCCAUGUUUUAGUAG
				hsa-miR-302c	UAAGUGCUUCCAUGUUUCAGUGG
				hsa-miR-302d	UAAGUGCUUCCAUGUUUGAGUGU
				hsa-miR-372	AAAGUGCUGCGACAUUUGAGCGU
				hsa-miR-373	GAAGUGCUUCGAUUUUGGGGUGU
				hsa-miR-520e	AAAGUGCUUCCUUUUUGAGGG
				hsa-miR-520a	AAAGUGCUUCCCUUUGGACUGU
				hsa-miR-520b	AAAGUGCUUCCUUUUAGAGGG
				hsa-miR-520c	AAAGUGCUUCCUUUUAGAGGGUU
				hsa-miR-520d	AAAGUGCUUCUCUUUGGUGGGUU

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: NFYA