SZGR2

Summary ?

GeneID	860
Symbol	RUNX2
Synonyms	AML3\|CBF-alpha-1\|CBFA1\|CCD\|CCD1\|CLCD\|OSF-2\|OSF2\|PEA2aA\|PEBP2aA
Description	runt related transcription factor 2
Reference	MIM:600211\|HGNC:HGNC:10472\|Ensembl:ENSG00000124813\|HPRD:02566\|Vega:OTTHUMG00000014774
Gene type	protein-coding
Map location	6p21
Pascal p-value	0.724
Fetal beta	0.237
DMG	1 (# studies)
eGene	Caudate basal ganglia

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:GWASdb	Genome-wide Association Studies	GWASdb records for schizophrenia
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.
GSMA_IIE	Genome scan meta-analysis (European-ancestry samples)	Psr: 0.04433
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenics,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
cg23376821	6	45391365	RUNX2	7.01E-8	-0.011	1.7E-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.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
TBX2	0.68	0.63
ITPKB	0.67	0.57
CHDH	0.66	0.54
TPCN1	0.65	0.56
GPR37L1	0.65	0.56
FAM38A	0.64	0.58
NACC2	0.64	0.56
GPER	0.64	0.60
PBXIP1	0.64	0.56
NFATC1	0.64	0.58

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
MED19	-0.49	-0.52
C18orf21	-0.47	-0.49
POLB	-0.46	-0.52
FRG1	-0.46	-0.52
COQ3	-0.46	-0.48
ING4	-0.46	-0.49
PAK1IP1	-0.45	-0.46
FARSB	-0.45	-0.47
ASNSD1	-0.45	-0.46
DUSP12	-0.45	-0.47

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0003682	chromatin binding	IEA		-
GO:0003700	transcription factor activity	IEA		-
GO:0003700	transcription factor activity	NAS		9182765
GO:0003702	RNA polymerase II transcription factor activity	TAS		9182762
GO:0005515	protein binding	IPI		11965546 \|12145306
GO:0005524	ATP binding	IEA		-
GO:0016563	transcription activator activity	IDA		11965546
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0001501	skeletal system development	IEA		-
GO:0001649	osteoblast differentiation	IEA		-
GO:0001649	osteoblast differentiation	TAS		12217689
GO:0002062	chondrocyte differentiation	IEA		-
GO:0006355	regulation of transcription, DNA-dependent	IEA		-
GO:0008284	positive regulation of cell proliferation	IEA		-
GO:0048469	cell maturation	IEA		-
GO:0016481	negative regulation of transcription	IDA		11965546
GO:0040036	regulation of fibroblast growth factor receptor signaling pathway	IEA		-
GO:0042487	regulation of odontogenesis of dentine-containing tooth	IEA		-
GO:0045879	negative regulation of smoothened signaling pathway	IEA		-
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005634	nucleus	IEA		-
GO:0005737	cytoplasm	IEA		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
CBFB	PEBP2B	core-binding factor, beta subunit	-	HPRD	12434156
CEBPB	C/EBP-beta \| CRP2 \| IL6DBP \| LAP \| MGC32080 \| NF-IL6 \| TCF5	CCAAT/enhancer binding protein (C/EBP), beta	-	HPRD	11668178
ETS1	ETS-1 \| EWSR2 \| FLJ10768	v-ets erythroblastosis virus E26 oncogene homolog 1 (avian)	-	HPRD,BioGRID	9794229
FOS	AP-1 \| C-FOS	v-fos FBJ murine osteosarcoma viral oncogene homolog	-	HPRD,BioGRID	11641401
HDAC3	HD3 \| RPD3 \| RPD3-2	histone deacetylase 3	Affinity Capture-Western Reconstituted Complex	BioGRID	15292260
HDAC6	FLJ16239 \| HD6 \| JM21	histone deacetylase 6	-	HPRD,BioGRID	12391164
JUN	AP-1 \| AP1 \| c-Jun	jun oncogene	-	HPRD,BioGRID	11274169 \|11641401
LEF1	DKFZp586H0919 \| TCF1ALPHA	lymphoid enhancer-binding factor 1	Reconstituted Complex	BioGRID	12551949
MSX2	CRS2 \| FPP \| HOX8 \| MSH \| PFM \| PFM1	msh homeobox 2	-	HPRD,BioGRID	11683913
MYST4	DKFZp313G1618 \| FLJ90335 \| KAT6B \| KIAA0383 \| MORF \| MOZ2 \| qkf \| querkopf	MYST histone acetyltransferase (monocytic leukemia) 4	-	HPRD,BioGRID	11965546
RB1	OSRC \| RB \| p105-Rb \| pRb \| pp110	retinoblastoma 1	Runx2 interacts with pRb.	BIND	15583032
SMAD1	BSP1 \| JV4-1 \| JV41 \| MADH1 \| MADR1	SMAD family member 1	Affinity Capture-Western	BioGRID	10531362 \|10962029
SMAD2	JV18 \| JV18-1 \| MADH2 \| MADR2 \| MGC22139 \| MGC34440 \| hMAD-2 \| hSMAD2	SMAD family member 2	-	HPRD,BioGRID	10531362
SMAD3	DKFZp586N0721 \| DKFZp686J10186 \| HSPC193 \| HsT17436 \| JV15-2 \| MADH3 \| MGC60396	SMAD family member 3	-	HPRD,BioGRID	10962029
SMAD5	DKFZp781C1895 \| DKFZp781O1323 \| Dwfc \| JV5-1 \| MADH5	SMAD family member 5	Affinity Capture-Western	BioGRID	10531362
THOC4	ALY \| BEF	THO complex 4	Reconstituted Complex	BioGRID	9119228
YAP1	YAP \| YAP2 \| YAP65 \| YKI	Yes-associated protein 1, 65kDa	-	HPRD,BioGRID	10228168

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
PID SMAD2 3NUCLEAR PATHWAY	82	63	All SZGR 2.0 genes in this pathway
PID FGF PATHWAY	55	37	All SZGR 2.0 genes in this pathway
PID RB 1PATHWAY	65	46	All SZGR 2.0 genes in this pathway
PID HES HEY PATHWAY	48	39	All SZGR 2.0 genes in this pathway
REACTOME YAP1 AND WWTR1 TAZ STIMULATED GENE EXPRESSION	24	16	All SZGR 2.0 genes in this pathway
REACTOME GENERIC TRANSCRIPTION PATHWAY	352	181	All SZGR 2.0 genes in this pathway
HOOI ST7 TARGETS UP	94	57	All SZGR 2.0 genes in this pathway
CHARAFE BREAST CANCER LUMINAL VS MESENCHYMAL DN	460	312	All SZGR 2.0 genes in this pathway
RODRIGUES DCC TARGETS DN	121	84	All SZGR 2.0 genes in this pathway
SENESE HDAC1 TARGETS DN	260	143	All SZGR 2.0 genes in this pathway
JAATINEN HEMATOPOIETIC STEM CELL UP	316	190	All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA ANAPLASTIC UP	722	443	All SZGR 2.0 genes in this pathway
GOZGIT ESR1 TARGETS DN	781	465	All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN DN	1781	1082	All SZGR 2.0 genes in this pathway
GRAESSMANN RESPONSE TO MC AND DOXORUBICIN DN	770	415	All SZGR 2.0 genes in this pathway
MARTIN INTERACT WITH HDAC	44	31	All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 2B	392	251	All SZGR 2.0 genes in this pathway
SCHLOSSER SERUM RESPONSE DN	712	443	All SZGR 2.0 genes in this pathway
MARTORIATI MDM4 TARGETS NEUROEPITHELIUM DN	164	111	All SZGR 2.0 genes in this pathway
SHETH LIVER CANCER VS TXNIP LOSS PAM2	153	102	All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS UP	1037	673	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
SHEN SMARCA2 TARGETS DN	357	212	All SZGR 2.0 genes in this pathway
OKUMURA INFLAMMATORY RESPONSE LPS	183	115	All SZGR 2.0 genes in this pathway
SANSOM APC TARGETS DN	366	238	All SZGR 2.0 genes in this pathway
MATSUDA NATURAL KILLER DIFFERENTIATION	475	313	All SZGR 2.0 genes in this pathway
ABRAHAM ALPC VS MULTIPLE MYELOMA UP	26	22	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE INCIPIENT UP	390	242	All SZGR 2.0 genes in this pathway
SU PANCREAS	54	30	All SZGR 2.0 genes in this pathway
KAYO CALORIE RESTRICTION MUSCLE DN	87	59	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP	1691	1088	All SZGR 2.0 genes in this pathway
RODWELL AGING KIDNEY UP	487	303	All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS STEM CELL AND PROGENITOR	681	420	All SZGR 2.0 genes in this pathway
BILD CTNNB1 ONCOGENIC SIGNATURE	82	52	All SZGR 2.0 genes in this pathway
RIGGI EWING SARCOMA PROGENITOR DN	191	123	All SZGR 2.0 genes in this pathway
LABBE TARGETS OF TGFB1 AND WNT3A UP	111	70	All SZGR 2.0 genes in this pathway
NAKAMURA METASTASIS MODEL DN	43	28	All SZGR 2.0 genes in this pathway
BOYLAN MULTIPLE MYELOMA C D DN	252	155	All SZGR 2.0 genes in this pathway
ZAIDI OSTEOBLAST TRANSCRIPTION FACTORS	14	12	All SZGR 2.0 genes in this pathway
GOLDRATH ANTIGEN RESPONSE	346	192	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
HAN SATB1 TARGETS UP	395	249	All SZGR 2.0 genes in this pathway
ONO AML1 TARGETS DN	41	25	All SZGR 2.0 genes in this pathway
ONO FOXP3 TARGETS DN	42	23	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 4HR DN	254	158	All SZGR 2.0 genes in this pathway
VERHAAK GLIOBLASTOMA MESENCHYMAL	216	130	All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 2 DN	336	211	All SZGR 2.0 genes in this pathway
DUAN PRDM5 TARGETS	79	52	All SZGR 2.0 genes in this pathway
PEDERSEN METASTASIS BY ERBB2 ISOFORM 1	46	33	All SZGR 2.0 genes in this pathway
WAKABAYASHI ADIPOGENESIS PPARG BOUND 8D	658	397	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-124.1	1529	1535	m8	hsa-miR-124a	UUAAGGCACGCGGUGAAUGCCA
miR-124/506	1529	1535	1A	hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
miR-124/506	1529	1535	1A	hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
miR-130/301	2728	2734	m8	hsa-miR-130a^brain	CAGUGCAAUGUUAAAAGGGCAU
				hsa-miR-301	CAGUGCAAUAGUAUUGUCAAAGC
				hsa-miR-130b^brain	CAGUGCAAUGAUGAAAGGGCAU
				hsa-miR-454-3p	UAGUGCAAUAUUGCUUAUAGGGUUU
miR-135	1015	1021	1A	hsa-miR-135a	UAUGGCUUUUUAUUCCUAUGUGA
				hsa-miR-135b	UAUGGCUUUUCAUUCCUAUGUG
				hsa-miR-135a	UAUGGCUUUUUAUUCCUAUGUGA
				hsa-miR-135b	UAUGGCUUUUCAUUCCUAUGUG
miR-137	1036	1042	m8	hsa-miR-137	UAUUGCUUAAGAAUACGCGUAG
miR-148/152	2729	2735	m8	hsa-miR-148a	UCAGUGCACUACAGAACUUUGU
				hsa-miR-152^brain	UCAGUGCAUGACAGAACUUGGG
				hsa-miR-148b	UCAGUGCAUCACAGAACUUUGU
miR-153	741	747	1A	hsa-miR-153	UUGCAUAGUCACAAAAGUGA
miR-19	2727	2733	m8	hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
miR-19	2727	2733	m8	hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
miR-203.1	934	940	m8	hsa-miR-203	UGAAAUGUUUAGGACCACUAG
miR-204/211	3653	3659	m8	hsa-miR-204^brain	UUCCCUUUGUCAUCCUAUGCCU
miR-204/211	3653	3659	m8	hsa-miR-211	UUCCCUUUGUCAUCCUUCGCCU
miR-205	1124	1131	1A,m8	hsa-miR-205	UCCUUCAUUCCACCGGAGUCUG
miR-218	1308	1315	1A,m8	hsa-miR-218^brain	UUGUGCUUGAUCUAACCAUGU
miR-221/222	3512	3518	1A	hsa-miR-221^brain	AGCUACAUUGUCUGCUGGGUUUC
miR-221/222	3512	3518	1A	hsa-miR-222^brain	AGCUACAUCUGGCUACUGGGUCUC
miR-224	623	629	m8	hsa-miR-224	CAAGUCACUAGUGGUUCCGUUUA
miR-23	1061	1067	m8	hsa-miR-23a^brain	AUCACAUUGCCAGGGAUUUCC
miR-23	1061	1067	m8	hsa-miR-23b^brain	AUCACAUUGCCAGGGAUUACC
miR-30-5p	3348	3354	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-323	1061	1067	1A	hsa-miR-323^brain	GCACAUUACACGGUCGACCUCU
miR-324-5p	2492	2498	m8	hsa-miR-324-5p	CGCAUCCCCUAGGGCAUUGGUGU
miR-330	391	398	1A,m8	hsa-miR-330^brain	GCAAAGCACACGGCCUGCAGAGA
miR-338	1242	1249	1A,m8	hsa-miR-338^brain	UCCAGCAUCAGUGAUUUUGUUGA
miR-369-3p	768	774	1A	hsa-miR-369-3p	AAUAAUACAUGGUUGAUCUUU
miR-374	768	774	m8	hsa-miR-374	UUAUAAUACAACCUGAUAAGUG
miR-383	639	645	1A	hsa-miR-383^brain	AGAUCAGAAGGUGAUUGUGGCU
miR-448	741	747	1A	hsa-miR-448	UUGCAUAUGUAGGAUGUCCCAU
miR-485-3p	1121	1128	1A,m8	hsa-miR-485-3p	GUCAUACACGGCUCUCCUCUCU
miR-495	3771	3777	1A	hsa-miR-495^brain	AAACAAACAUGGUGCACUUCUUU
miR-543	2510	2516	1A	hsa-miR-543	AAACAUUCGCGGUGCACUUCU
miR-9	2764	2770	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: RUNX2