Gene Page: RUNX3

Summary ?
GeneID864
SymbolRUNX3
SynonymsAML2|CBFA3|PEBP2aC
Descriptionrunt related transcription factor 3
ReferenceMIM:600210|HGNC:HGNC:10473|Ensembl:ENSG00000020633|HPRD:02565|Vega:OTTHUMG00000003316
Gene typeprotein-coding
Map location1p36
Pascal p-value0.317
TADA p-value0.012
Fetal beta0.053
DMG1 (# studies)

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:vanEijk_2014Genome-wide DNA methylation analysisThis dataset includes 432 differentially methylated CpG sites corresponding to 391 unique transcripts between schizophrenia patients (n=260) and unaffected controls (n=250). 2
DNM:Gulsuner_2013Whole Exome Sequencing analysis155 DNMs identified by exome sequencing of quads or trios of schizophrenia individuals and their parents.

Section I. Genetics and epigenetics annotation

@DNM table

GeneChromosomePositionRefAltTranscriptAA changeMutation typeSiftCG46TraitStudy
RUNX3chr125233863CTNM_001031680
NM_004350		p.211R>H
p.197R>H		missense
missense		SchizophreniaDNM:Gulsuner_2013

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg06037693125292072RUNX37.24E-8-8.177DMG:vanEijk_2014
cg16529592125292215RUNX32E-6-8.26DMG:vanEijk_2014


Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

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
GenePearson's Correlation Spearman's Correlation
LRCH10.940.92
SSBP20.940.89
EIF4B0.940.91
SEMA3A0.930.91
USP30.930.88
SLAIN20.920.93
XRN20.920.95
PRRC10.920.93
KDM5B0.920.95
C9orf970.920.93
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
LHPP-0.66-0.66
TNFSF12-0.65-0.71
C5orf53-0.65-0.81
FBXO2-0.65-0.70
HLA-F-0.64-0.83
SERPINB6-0.64-0.74
AIFM3-0.64-0.82
SLC16A11-0.63-0.70
ALDOC-0.63-0.74
PTH1R-0.63-0.76

Section IV. Protein-protein interaction annotation

InteractorsAliases BOfficial full name BExperimentalSourcePubMed ID
CBFBPEBP2Bcore-binding factor, beta subunit-HPRD7622058 
CBFBPEBP2Bcore-binding factor, beta subunitCbf-beta interacts with AML2. This interaction was modeled on a demonstrated interaction between mouse Cbf-beta and human AML2.BIND9751710 
EP300KAT3B | p300E1A binding protein p300-HPRD15138260 
HDAC1DKFZp686H12203 | GON-10 | HD1 | RPD3 | RPD3L1histone deacetylase 1-HPRD15138260 
HDAC2RPD3 | YAF1histone deacetylase 2-HPRD15138260 
HDAC4HA6116 | HD4 | HDAC-A | HDACA | KIAA0288histone deacetylase 4-HPRD15138260 
HDAC5FLJ90614 | HD5 | NY-CO-9histone deacetylase 5-HPRD15138260 
PHB2BAP | BCAP37 | Bap37 | MGC117268 | PNAS-141 | REA | p22prohibitin 2Affinity Capture-MSBioGRID17353931 
SMAD1BSP1 | JV4-1 | JV41 | MADH1 | MADR1SMAD family member 1Affinity Capture-WesternBioGRID10531362 
SMAD2JV18 | JV18-1 | MADH2 | MADR2 | MGC22139 | MGC34440 | hMAD-2 | hSMAD2SMAD family member 2Affinity Capture-WesternBioGRID10531362 
SMAD3DKFZp586N0721 | DKFZp686J10186 | HSPC193 | HsT17436 | JV15-2 | MADH3 | MGC60396SMAD family member 3-HPRD15138260 
SMAD3DKFZp586N0721 | DKFZp686J10186 | HSPC193 | HsT17436 | JV15-2 | MADH3 | MGC60396SMAD family member 3Affinity Capture-WesternBioGRID10531362 
SMAD5DKFZp781C1895 | DKFZp781O1323 | Dwfc | JV5-1 | MADH5SMAD family member 5Affinity Capture-WesternBioGRID10531362 
SMURF1KIAA1625SMAD specific E3 ubiquitin protein ligase 1-HPRD15138260 
SMURF2DKFZp686F0270 | MGC138150SMAD specific E3 ubiquitin protein ligase 2-HPRD15138260 
TLE1ESG | ESG1 | GRG1transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila)AML2 interacts with TLE1.BIND9751710 
TLE1ESG | ESG1 | GRG1transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila)-HPRD,BioGRID9751710 
YAP1YAP | YAP2 | YAP65 | YKIYes-associated protein 1, 65kDaReconstituted ComplexBioGRID10228168 


Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
PID SMAD2 3NUCLEAR PATHWAY 8263All SZGR 2.0 genes in this pathway
HOLLMANN APOPTOSIS VIA CD40 UP 201125All SZGR 2.0 genes in this pathway
GARY CD5 TARGETS UP 473314All SZGR 2.0 genes in this pathway
CHARAFE BREAST CANCER LUMINAL VS BASAL DN 455304All SZGR 2.0 genes in this pathway
OSMAN BLADDER CANCER UP 404246All SZGR 2.0 genes in this pathway
GINESTIER BREAST CANCER ZNF217 AMPLIFIED DN 335193All SZGR 2.0 genes in this pathway
HOEBEKE LYMPHOID STEM CELL UP 9564All SZGR 2.0 genes in this pathway
TONKS TARGETS OF RUNX1 RUNX1T1 FUSION HSC DN 187115All SZGR 2.0 genes in this pathway
CHOW RASSF1 TARGETS DN 2919All SZGR 2.0 genes in this pathway
GAUSSMANN MLL AF4 FUSION TARGETS B UP 2616All SZGR 2.0 genes in this pathway
LASTOWSKA NEUROBLASTOMA COPY NUMBER DN 800473All SZGR 2.0 genes in this pathway
MUELLER METHYLATED IN GLIOBLASTOMA 4022All SZGR 2.0 genes in this pathway
PEREZ TP63 TARGETS 355243All SZGR 2.0 genes in this pathway
MARTIN INTERACT WITH HDAC 4431All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 2B 392251All SZGR 2.0 genes in this pathway
DIRMEIER LMP1 RESPONSE LATE UP 5741All SZGR 2.0 genes in this pathway
AMUNDSON RESPONSE TO ARSENITE 217143All SZGR 2.0 genes in this pathway
LI WILMS TUMOR VS FETAL KIDNEY 2 DN 5142All SZGR 2.0 genes in this pathway
BENPORATH ES CORE NINE CORRELATED 10068All SZGR 2.0 genes in this pathway
AMIT EGF RESPONSE 60 HELA 4632All SZGR 2.0 genes in this pathway
AMIT EGF RESPONSE 120 HELA 6947All SZGR 2.0 genes in this pathway
ZHANG TARGETS OF EWSR1 FLI1 FUSION 8868All SZGR 2.0 genes in this pathway
VERHAAK AML WITH NPM1 MUTATED DN 246180All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 20HR UP 240152All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 16HR UP 225139All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 48HR UP 180125All SZGR 2.0 genes in this pathway
VISALA AGING LYMPHOCYTE DN 1910All SZGR 2.0 genes in this pathway
RODWELL AGING KIDNEY UP 487303All SZGR 2.0 genes in this pathway
BILD E2F3 ONCOGENIC SIGNATURE 246153All SZGR 2.0 genes in this pathway
LOPES METHYLATED IN COLON CANCER DN 2826All SZGR 2.0 genes in this pathway
WALLACE PROSTATE CANCER RACE UP 299167All SZGR 2.0 genes in this pathway
CHENG IMPRINTED BY ESTRADIOL 11068All SZGR 2.0 genes in this pathway
ACEVEDO METHYLATED IN LIVER CANCER DN 940425All SZGR 2.0 genes in this pathway
HOQUE METHYLATED IN CANCER 5645All SZGR 2.0 genes in this pathway
SMID BREAST CANCER RELAPSE IN BONE DN 315197All SZGR 2.0 genes in this pathway
SMID BREAST CANCER LUMINAL B DN 564326All SZGR 2.0 genes in this pathway
SMID BREAST CANCER NORMAL LIKE UP 476285All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL UP 648398All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO CSF2RB AND IL4 UP 338225All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO HGF DN 235144All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO HGF VS CSF2RB AND IL4 DN 245150All SZGR 2.0 genes in this pathway
FINAK BREAST CANCER SDPP SIGNATURE 2611All SZGR 2.0 genes in this pathway
ZHAN EARLY DIFFERENTIATION GENES DN 4229All SZGR 2.0 genes in this pathway
VALK AML CLUSTER 9 3526All SZGR 2.0 genes in this pathway
JISON SICKLE CELL DISEASE DN 18197All SZGR 2.0 genes in this pathway
ONO AML1 TARGETS DN 4125All SZGR 2.0 genes in this pathway
ONO FOXP3 TARGETS DN 4223All SZGR 2.0 genes in this pathway
FONTAINE PAPILLARY THYROID CARCINOMA DN 8053All SZGR 2.0 genes in this pathway
MARTENS BOUND BY PML RARA FUSION 456287All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP D 280158All SZGR 2.0 genes in this pathway
TORCHIA TARGETS OF EWSR1 FLI1 FUSION DN 321200All SZGR 2.0 genes in this pathway
ALFANO MYC TARGETS 239156All SZGR 2.0 genes in this pathway
BOSCO TH1 CYTOTOXIC MODULE 11462All SZGR 2.0 genes in this pathway