SZGR2

Summary ?

GeneID	5080
Symbol	PAX6
Synonyms	AN\|AN2\|D11S812E\|FVH1\|MGDA\|WAGR
Description	paired box 6
Reference	MIM:607108\|HGNC:HGNC:8620\|Ensembl:ENSG00000007372\|HPRD:06167\|
Gene type	protein-coding
Map location	11p13
Pascal p-value	0.048
Sherlock p-value	0.382
Fetal beta	1.225
DMG	2 (# studies)
eGene	Nucleus accumbens basal ganglia Myers' cis & trans

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.	3
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).	3
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
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenias	Click to show details
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 1

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg15778437	11	31839521	PAX6	2.04E-5	-0.414	0.016	DMG:Wockner_2014
cg17280740	11	31840862	PAX6	5.882E-4	0.326	0.05	DMG:Wockner_2014
cg13023210	11	31821452	PAX6	5.84E-9	-0.026	3.16E-6	DMG:Jaffe_2016

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs17392743	chr1	54764240	PAX6	5080	0.04	trans
rs2502827	chr1	176044216	PAX6	5080	0.09	trans
rs17572651	chr1	218943612	PAX6	5080	0	trans
rs16829545	chr2	151977407	PAX6	5080	1.783E-10	trans
rs3845734	chr2	171125572	PAX6	5080	0	trans
rs1967327	chr2	179314358	PAX6	5080	0.19	trans
rs7584986	chr2	184111432	PAX6	5080	5.069E-8	trans
rs17762315	chr5	76807576	PAX6	5080	0.03	trans
rs7729096	chr5	76835927	PAX6	5080	0.16	trans
rs2393316	chr10	59333070	PAX6	5080	0.05	trans
rs17104720	chr14	77127308	PAX6	5080	0.03	trans
rs16955618	chr15	29937543	PAX6	5080	1.26E-19	trans
rs1041786	chr21	22617710	PAX6	5080	0.04	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:0003700	transcription factor activity	TAS		10441571 \|10747901
GO:0005515	protein binding	IPI		16098226
GO:0043565	sequence-specific DNA binding	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007417	central nervous system development	TAS	Brain (GO term level: 6)	10747901
GO:0001654	eye development	TAS		10747901
GO:0006355	regulation of transcription, DNA-dependent	IEA		-
GO:0009887	organ morphogenesis	TAS		10441571
GO:0007601	visual perception	TAS		10441571
GO:0007275	multicellular organismal development	IEA		-
GO:0030154	cell differentiation	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005634	nucleus	IEA		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
CDX2	CDX-3 \| CDX3	caudal type homeobox 2	-	HPRD,BioGRID	10506141
EN1	-	engrailed homeobox 1	Reconstituted Complex	BioGRID	11069920
EP300	KAT3B \| p300	E1A binding protein p300	Affinity Capture-Western Reconstituted Complex	BioGRID	10506141
HOXB1	HOX2 \| HOX2I \| Hox-2.9 \| MGC116843 \| MGC116844 \| MGC116845	homeobox B1	-	HPRD,BioGRID	11069920
HOXB1	HOX2 \| HOX2I \| Hox-2.9 \| MGC116843 \| MGC116844 \| MGC116845	homeobox B1	Pax6 interacts with HoxB1. This interaction was modeled on a demonstrated interaction between zebrafish Pax6 and human HoxB1.	BIND	11069920
IPO13	IMP13 \| KAP13 \| KIAA0724 \| RANBP13	importin 13	Kap13 interacts with Pax6.	BIND	15143176
IPO13	IMP13 \| KAP13 \| KIAA0724 \| RANBP13	importin 13	Affinity Capture-Western Reconstituted Complex Two-hybrid	BioGRID	15143176 \|16189514
LHX2	LH2 \| MGC138390 \| hLhx2	LIM homeobox 2	Reconstituted Complex	BioGRID	11069920
MAFG	MGC13090 \| MGC20149	v-maf musculoaponeurotic fibrosarcoma oncogene homolog G (avian)	-	HPRD,BioGRID	11036080
MITF	MI \| WS2A \| bHLHe32	microphthalmia-associated transcription factor	-	HPRD,BioGRID	11350962
PAX6	AN \| AN2 \| D11S812E \| MGC17209 \| MGDA \| WAGR	paired box 6	Affinity Capture-Western Reconstituted Complex	BioGRID	11069920
PBX1	DKFZp686B09108 \| MGC126627	pre-B-cell leukemia homeobox 1	Pax6 interacts with Pbx1. This interaction was modeled on a demonstrated interaction between zebrafish Pax6 and human Pbx1.	BIND	11069920
PKNOX1	PREP1 \| pkonx1c	PBX/knotted 1 homeobox 1	Reconstituted Complex	BioGRID	11069920
PROX1	-	prospero homeobox 1	Reconstituted Complex	BioGRID	11069920
RAX	MCOP3 \| RX	retina and anterior neural fold homeobox	-	HPRD,BioGRID	11069920
RB1	OSRC \| RB \| p105-Rb \| pRb \| pp110	retinoblastoma 1	Reconstituted Complex	BioGRID	10359315
SIX3	HPE2	SIX homeobox 3	-	HPRD,BioGRID	11069920
SOX2	ANOP3 \| MCOPS3 \| MGC2413	SRY (sex determining region Y)-box 2	-	HPRD,BioGRID	11358870 \|12710953 \|12923055
SOX3	GHDX \| MRGH \| PHP \| PHPX \| SOXB	SRY (sex determining region Y)-box 3	-	HPRD	12710953
TAF1	BA2R \| CCG1 \| CCGS \| DYT3 \| KAT4 \| N-TAF1 \| NSCL2 \| OF \| P250 \| TAF2A \| TAFII250	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	Affinity Capture-Western	BioGRID	10359315
TBP	GTF2D \| GTF2D1 \| MGC117320 \| MGC126054 \| MGC126055 \| SCA17 \| TFIID	TATA box binding protein	-	HPRD,BioGRID	10359315
VSX2	CHX10 \| HOX10 \| MCOP2 \| MCOPCB3 \| RET1	visual system homeobox 2	Reconstituted Complex	BioGRID	11069920

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG MATURITY ONSET DIABETES OF THE YOUNG	25	19	All SZGR 2.0 genes in this pathway
PID CDC42 PATHWAY	70	51	All SZGR 2.0 genes in this pathway
REACTOME DEVELOPMENTAL BIOLOGY	396	292	All SZGR 2.0 genes in this pathway
REACTOME REGULATION OF BETA CELL DEVELOPMENT	30	23	All SZGR 2.0 genes in this pathway
REACTOME REGULATION OF GENE EXPRESSION IN BETA CELLS	20	15	All SZGR 2.0 genes in this pathway
REACTOME INTEGRATION OF ENERGY METABOLISM	120	84	All SZGR 2.0 genes in this pathway
REACTOME REGULATION OF INSULIN SECRETION	93	65	All SZGR 2.0 genes in this pathway
REACTOME SYNTHESIS SECRETION AND INACTIVATION OF GIP	14	8	All SZGR 2.0 genes in this pathway
REACTOME INCRETIN SYNTHESIS SECRETION AND INACTIVATION	22	14	All SZGR 2.0 genes in this pathway
REACTOME SYNTHESIS SECRETION AND INACTIVATION OF GLP1	19	12	All SZGR 2.0 genes in this pathway
DOANE BREAST CANCER ESR1 DN	48	28	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
YEMELYANOV GR TARGETS DN	10	8	All SZGR 2.0 genes in this pathway
GRUETZMANN PANCREATIC CANCER DN	203	134	All SZGR 2.0 genes in this pathway
SCHLESINGER METHYLATED DE NOVO IN CANCER	88	64	All SZGR 2.0 genes in this pathway
KOYAMA SEMA3B TARGETS UP	292	168	All SZGR 2.0 genes in this pathway
BENPORATH SUZ12 TARGETS	1038	678	All SZGR 2.0 genes in this pathway
BENPORATH EED TARGETS	1062	725	All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3	1118	744	All SZGR 2.0 genes in this pathway
BENPORATH PRC2 TARGETS	652	441	All SZGR 2.0 genes in this pathway
BENPORATH ES CORE NINE CORRELATED	100	68	All SZGR 2.0 genes in this pathway
TESAR ALK TARGETS HUMAN ES 5D UP	5	5	All SZGR 2.0 genes in this pathway
TARTE PLASMA CELL VS PLASMABLAST UP	398	262	All SZGR 2.0 genes in this pathway
WEBER METHYLATED IN COLON CANCER	18	13	All SZGR 2.0 genes in this pathway
SATO SILENCED BY METHYLATION IN PANCREATIC CANCER 2	50	34	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP	1691	1088	All SZGR 2.0 genes in this pathway
SATO SILENCED EPIGENETICALLY IN PANCREATIC CANCER	49	30	All SZGR 2.0 genes in this pathway
SATO SILENCED BY METHYLATION IN PANCREATIC CANCER 1	419	273	All SZGR 2.0 genes in this pathway
TESAR ALK TARGETS EPISC 4D UP	7	6	All SZGR 2.0 genes in this pathway
TESAR ALK AND JAK TARGETS MOUSE ES D4 UP	5	5	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
SMID BREAST CANCER RELAPSE IN BONE DN	315	197	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER LUMINAL B DN	564	326	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL UP	648	398	All SZGR 2.0 genes in this pathway
ZHOU PANCREATIC ENDOCRINE PROGENITOR	14	11	All SZGR 2.0 genes in this pathway
ZHOU PANCREATIC BETA CELL	11	9	All SZGR 2.0 genes in this pathway
HSIAO HOUSEKEEPING GENES	389	245	All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K4ME3 AND H3K27ME3	1069	729	All SZGR 2.0 genes in this pathway
DUAN PRDM5 TARGETS	79	52	All SZGR 2.0 genes in this pathway
HUANG GATA2 TARGETS UP	149	96	All SZGR 2.0 genes in this pathway
WANG MLL TARGETS	289	188	All SZGR 2.0 genes in this pathway
ROLEF GLIS3 TARGETS	37	29	All SZGR 2.0 genes in this pathway
RAO BOUND BY SALL4 ISOFORM B	517	302	All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY	1725	838	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-129-5p	572	579	1A,m8	hsa-miR-129^brain	CUUUUUGCGGUCUGGGCUUGC
miR-129-5p	572	579	1A,m8	hsa-miR-129-5p	CUUUUUGCGGUCUGGGCUUGCU
miR-182	975	981	1A	hsa-miR-182	UUUGGCAAUGGUAGAACUCACA
miR-190	937	944	1A,m8	hsa-miR-190	UGAUAUGUUUGAUAUAUUAGGU
miR-363	570	576	1A	hsa-miR-363	AUUGCACGGUAUCCAUCUGUAA
miR-365	266	272	m8	hsa-miR-365	UAAUGCCCCUAAAAAUCCUUAU
miR-369-3p	251	257	m8	hsa-miR-369-3p	AAUAAUACAUGGUUGAUCUUU
miR-375	207	213	1A	hsa-miR-375	UUUGUUCGUUCGGCUCGCGUGA
miR-450	572	578	1A	hsa-miR-450	UUUUUGCGAUGUGUUCCUAAUA
miR-7	681	687	m8	hsa-miR-7^SZ	UGGAAGACUAGUGAUUUUGUUG
miR-96	975	981	1A	hsa-miR-96^brain	UUUGGCACUAGCACAUUUUUGC

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: PAX6