Summary ?
GeneID9612
SymbolNCOR2
SynonymsCTG26|N-CoR2|SMAP270|SMRT|SMRTE|SMRTE-tau|TNRC14|TRAC|TRAC-1|TRAC1
Descriptionnuclear receptor corepressor 2
ReferenceMIM:600848|HGNC:HGNC:7673|Ensembl:ENSG00000196498|HPRD:02910|Vega:OTTHUMG00000150455
Gene typeprotein-coding
Map location12q24
Pascal p-value0.008
Sherlock p-value0.704
Fetal beta-0.704
DMG2 (# studies)
eGeneMyers' cis & trans
SupportCompositeSet
Darnell FMRP targets

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Montano_2016Genome-wide DNA methylation analysisThis dataset includes 172 replicated associations between CpGs with schizophrenia. 6
DMG:Wockner_2014Genome-wide DNA methylation analysisThis dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24). 6
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
NCOR2chr12124856705CTNM_001077261
NM_001206654
NM_006312
.
.
.
silent
silent
silent
SchizophreniaDNM:Fromer_2014
NCOR2chr12124821527GANM_001077261
NM_001206654
NM_006312
p.1953R>C
p.1953R>C
p.1963R>C
missense
missense
missense
SchizophreniaDNM:Gulsuner_2013

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg2638512612124912021NCOR24.99E-70.0060.014DMG:Montano_2016
cg2743187712124911924NCOR22.29E-50.0050.066DMG:Montano_2016
cg1131105312124912049NCOR26.7E-50.0060.105DMG:Montano_2016
ch.12.2647993F12124837365NCOR21.157E-4-0.6490.029DMG:Wockner_2014
cg2638512612124912021NCOR22.517E-40.4890.037DMG:Wockner_2014
cg0994221012124965227NCOR23.422E-4-0.480.041DMG:Wockner_2014

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs11057881chr12125371972NCOR296120.09cis
rs13297121chr971994881NCOR296120.1trans

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.

No co-expressed genes in brain regions


Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0004872receptor activityIEA-
GO:0003677DNA bindingIEA-
GO:0003714transcription corepressor activityTAS7566127 
GO:0005112Notch bindingIPI10713164 
GO:0005515protein bindingIPI10713164 |15016912 
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0006355regulation of transcription, DNA-dependentIEA-
GO:0045449regulation of transcriptionIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005634nucleusTAS10097068 
GO:0005730nucleolusIDA18029348 

Section IV. Protein-protein interaction annotation

InteractorsAliases BOfficial full name BExperimentalSourcePubMed ID
ARAIS | DHTR | HUMARA | KD | NR3C4 | SBMA | SMAX1 | TFMandrogen receptorAffinity Capture-Western
Co-localization
Reconstituted Complex
Two-hybrid
BioGRID11923464 |12441355 
|14593076 
BCL6BCL5 | BCL6A | LAZ3 | ZBTB27 | ZNF51B-cell CLL/lymphoma 6-HPRD,BioGRID9765306 
BCL6BCL5 | BCL6A | LAZ3 | ZBTB27 | ZNF51B-cell CLL/lymphoma 6The lateral groove motif in the BTB domain of BCL6 interacts with the BBD motif of SMRT.BIND15531890 
BIRC3AIP1 | API2 | CIAP2 | HAIP1 | HIAP1 | MALT2 | MIHC | RNF49baculoviral IAP repeat-containing 3The cIAP-2 promoter interacts with SMRT.BIND15494311 
CBFA2T2DKFZp313F2116 | EHT | MTGR1 | ZMYND3core-binding factor, runt domain, alpha subunit 2; translocated to, 2-HPRD12242670 
CCL3G0S19-1 | LD78ALPHA | MIP-1-alpha | MIP1A | SCYA3chemokine (C-C motif) ligand 3SMRT interacts with the CCL3 promoter region.BIND15531890 
CCND2KIAK0002 | MGC102758cyclin D2SMRT interacts with the CCND2 promoter region.BIND15531890 
CDKN2AARF | CDK4I | CDKN2 | CMM2 | INK4 | INK4a | MLM | MTS1 | TP16 | p14 | p14ARF | p16 | p16INK4 | p16INK4a | p19cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)NCOR2 (SMRT) interacts with p-p14(ARF) (p14(ARF) promoter).BIND15729358 
CHUKIKBKA | IKK-alpha | IKK1 | IKKA | NFKBIKA | TCF16conserved helix-loop-helix ubiquitous kinaseIKK-alpha phosphorylates SMRT.BIND15494311 
CIR-CBF1 interacting corepressor-HPRD,BioGRID11509665 
ESR1DKFZp686N23123 | ER | ESR | ESRA | Era | NR3A1estrogen receptor 1ESR1 (ER-alpha) interacts with NCOR2 (SMRT). This interaction was modeled on a demonstrated interaction between ESR1 from an unspecified species and NCOR2 from an unspecified species.BIND12738788 
ESR1DKFZp686N23123 | ER | ESR | ESRA | Era | NR3A1estrogen receptor 1-HPRD9702189 
FOSAP-1 | C-FOSv-fos FBJ murine osteosarcoma viral oncogene homolog-HPRD,BioGRID10777532 
HDAC1DKFZp686H12203 | GON-10 | HD1 | RPD3 | RPD3L1histone deacetylase 1Affinity Capture-Western
Co-purification
BioGRID11013263 |11739383 
HDAC10DKFZp761B039 | MGC149722histone deacetylase 10-HPRD,BioGRID11739383 
HDAC2RPD3 | YAF1histone deacetylase 2Co-purificationBioGRID11013263 
HDAC3HD3 | RPD3 | RPD3-2histone deacetylase 3Affinity Capture-MS
Affinity Capture-Western
Co-fractionation
Co-purification
Reconstituted Complex
BioGRID10809664 |10944117 
|11013263 |11804585 
|12502735 |12628926 
|14527417 
HDAC4HA6116 | HD4 | HDAC-A | HDACA | KIAA0288histone deacetylase 4-HPRD,BioGRID11804585 
HDAC5FLJ90614 | HD5 | NY-CO-9histone deacetylase 5-HPRD10869435 
HDAC5FLJ90614 | HD5 | NY-CO-9histone deacetylase 5Reconstituted Complex
Two-hybrid
BioGRID10640275 
HDAC7DKFZp586J0917 | FLJ99588 | HD7A | HDAC7Ahistone deacetylase 7Affinity Capture-WesternBioGRID11466315 
IKZF1Hs.54452 | IK1 | IKAROS | LYF1 | PRO0758 | ZNFN1A1 | hIk-1IKAROS family zinc finger 1 (Ikaros)Affinity Capture-WesternBioGRID11959865 
IL8CXCL8 | GCP-1 | GCP1 | LECT | LUCT | LYNAP | MDNCF | MONAP | NAF | NAP-1 | NAP1interleukin 8The IL-8 promoter interacts with SMRT.BIND15494311 
INPP5KPPS | SKIPinositol polyphosphate-5-phosphatase KTwo-hybridBioGRID11509665 
JUNAP-1 | AP1 | c-Junjun oncogeneReconstituted Complex
Two-hybrid
BioGRID10777532 
MYBL2B-MYB | BMYB | MGC15600v-myb myeloblastosis viral oncogene homolog (avian)-like 2-HPRD11997503 
MYOD1MYF3 | MYOD | PUM | bHLHc1myogenic differentiation 1-HPRD10406466 
NCOA3ACTR | AIB-1 | AIB1 | CAGH16 | CTG26 | KAT13B | MGC141848 | RAC3 | SRC3 | TNRC14 | TNRC16 | TRAM-1 | pCIPnuclear receptor coactivator 3-HPRD9267036 
NCOR1KIAA1047 | MGC104216 | N-CoR | TRAC1 | hCIT529I10 | hN-CoRnuclear receptor co-repressor 1Co-fractionationBioGRID10944117 
NFKB1DKFZp686C01211 | EBP-1 | KBF1 | MGC54151 | NF-kappa-B | NFKB-p105 | NFKB-p50 | p105nuclear factor of kappa light polypeptide gene enhancer in B-cells 1-HPRD10777532 
NFKBIAIKBA | MAD-3 | NFKBInuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alphaAffinity Capture-WesternBioGRID12589049 
NR3C1GCCR | GCR | GR | GRLnuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)-HPRD,BioGRID12011091 
NR4A1GFRP1 | HMR | MGC9485 | N10 | NAK-1 | NGFIB | NP10 | NUR77 | TR3nuclear receptor subfamily 4, group A, member 1-HPRD,BioGRID11559707 
PMLMYL | PP8675 | RNF71 | TRIM19promyelocytic leukemia-HPRD,BioGRID11585900 
POU2F1OCT1 | OTF1POU class 2 homeobox 1-HPRD,BioGRID11134019 
PPARAMGC2237 | MGC2452 | NR1C1 | PPAR | hPPARperoxisome proliferator-activated receptor alpha-HPRD,BioGRID11845213 
PPARDFAAR | MGC3931 | NR1C2 | NUC1 | NUCI | NUCII | PPAR-beta | PPARBperoxisome proliferator-activated receptor delta-HPRD,BioGRID11867749 
PPARDFAAR | MGC3931 | NR1C2 | NUC1 | NUCI | NUCII | PPAR-beta | PPARBperoxisome proliferator-activated receptor deltaPPAR-delta interacts with SMRT. This interaction was modelled on a demonstrated interaction between PPAR-delta and SMRT from unspecified sources.BIND12970571 
RARANR1B1 | RARretinoic acid receptor, alphaAffinity Capture-Western
Reconstituted Complex
BioGRID9256429 |11929748 
RARANR1B1 | RARretinoic acid receptor, alphaNCOR2 (SMRT) interacts with p-RAR-alpha2 (RAR-alpha2 promoter).BIND15729358 
RBPJCBF1 | IGKJRB | IGKJRB1 | KBF2 | MGC61669 | RBP-J | RBPJK | RBPSUH | SUH | cslrecombination signal binding protein for immunoglobulin kappa J region-HPRD,BioGRID11509665 
RELAMGC131774 | NFKB3 | p65v-rel reticuloendotheliosis viral oncogene homolog A (avian)-HPRD,BioGRID12589049 
RUNX1T1AML1T1 | CBFA2T1 | CDR | ETO | MGC2796 | MTG8 | MTG8b | ZMYND2runt-related transcription factor 1; translocated to, 1 (cyclin D-related)-HPRD,BioGRID11113190 
SAP30-Sin3A-associated protein, 30kDa-HPRD9702189 
SAP30-Sin3A-associated protein, 30kDaCo-purificationBioGRID11013263 
SIN3ADKFZp434K2235 | FLJ90319 | KIAA0700SIN3 homolog A, transcription regulator (yeast)Co-fractionation
Reconstituted Complex
BioGRID10640275 |10944117 
SIRT1SIR2L1sirtuin (silent mating type information regulation 2 homolog) 1 (S. cerevisiae)Sirt1 interacts with SMRT.BIND15175761 
SMARCA4BAF190 | BRG1 | FLJ39786 | SNF2 | SNF2-BETA | SNF2L4 | SNF2LB | SWI2 | hSNF2bSWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4Co-fractionationBioGRID10944117 
SNW1Bx42 | MGC119379 | NCOA-62 | PRPF45 | Prp45 | SKIIP | SKIPSNW domain containing 1Affinity Capture-Western
in vitro
in vivo
Two-hybrid
BioGRID10644367 |10713164 
SNW1Bx42 | MGC119379 | NCOA-62 | PRPF45 | Prp45 | SKIIP | SKIPSNW domain containing 1-HPRD10713164 |11509665 
SPENKIAA0929 | MINT | RP1-134O19.1 | SHARPspen homolog, transcriptional regulator (Drosophila)-HPRD,BioGRID11331609 
SRFMCM1serum response factor (c-fos serum response element-binding transcription factor)-HPRD,BioGRID10777532 
STAT5AMGF | STAT5signal transducer and activator of transcription 5A-HPRD11726519 
STAT5BSTAT5signal transducer and activator of transcription 5B-HPRD11726519 
TBL1XEBI | SMAP55 | TBL1transducin (beta)-like 1X-linked-HPRD,BioGRID10809664 
THRBERBA-BETA | ERBA2 | GRTH | MGC126109 | MGC126110 | NR1A2 | PRTH | THR1 | THRB1 | THRB2thyroid hormone receptor, beta (erythroblastic leukemia viral (v-erb-a) oncogene homolog 2, avian)Reconstituted ComplexBioGRID9751500 
VDRNR1I1vitamin D (1,25- dihydroxyvitamin D3) receptorReconstituted ComplexBioGRID12460926 
YWHAE14-3-3E | FLJ45465 | KCIP-1 | MDCR | MDStyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide14-3-3-epsilon interacts with SMRT.BIND15494311 
ZBTB16PLZF | ZNF145zinc finger and BTB domain containing 16-HPRD9256429 |14982881 
ZBTB16PLZF | ZNF145zinc finger and BTB domain containing 16Affinity Capture-Western
Reconstituted Complex
Two-hybrid
BioGRID9256429 |9765306 
|14982881 
ZBTB16PLZF | ZNF145zinc finger and BTB domain containing 16SMRT interacts with PLZF. This interaction was modelled on a demonstrated interaction between SMRT and PLZF from unspecified species.BIND9486654 


Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG NOTCH SIGNALING PATHWAY 4735All SZGR 2.0 genes in this pathway
BIOCARTA CARM ER PATHWAY 3527All SZGR 2.0 genes in this pathway
BIOCARTA EGFR SMRTE PATHWAY 1111All SZGR 2.0 genes in this pathway
BIOCARTA PPARA PATHWAY 5843All SZGR 2.0 genes in this pathway
BIOCARTA ETS PATHWAY 1812All SZGR 2.0 genes in this pathway
BIOCARTA RARRXR PATHWAY 159All SZGR 2.0 genes in this pathway
PID NOTCH PATHWAY 5949All SZGR 2.0 genes in this pathway
PID HDAC CLASSII PATHWAY 3427All SZGR 2.0 genes in this pathway
PID HDAC CLASSI PATHWAY 6650All SZGR 2.0 genes in this pathway
PID RXR VDR PATHWAY 2624All SZGR 2.0 genes in this pathway
PID ERA GENOMIC PATHWAY 6537All SZGR 2.0 genes in this pathway
PID RETINOIC ACID PATHWAY 3023All SZGR 2.0 genes in this pathway
PID HES HEY PATHWAY 4839All SZGR 2.0 genes in this pathway
REACTOME DEVELOPMENTAL BIOLOGY 396292All SZGR 2.0 genes in this pathway
REACTOME NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION 4628All SZGR 2.0 genes in this pathway
REACTOME SIGNALING BY NOTCH1 7046All SZGR 2.0 genes in this pathway
REACTOME TRANSCRIPTIONAL ACTIVITY OF SMAD2 SMAD3 SMAD4 HETEROTRIMER 3826All SZGR 2.0 genes in this pathway
REACTOME DOWNREGULATION OF SMAD2 3 SMAD4 TRANSCRIPTIONAL ACTIVITY 2014All SZGR 2.0 genes in this pathway
REACTOME GENERIC TRANSCRIPTION PATHWAY 352181All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF LIPIDS AND LIPOPROTEINS 478302All SZGR 2.0 genes in this pathway
REACTOME FATTY ACID TRIACYLGLYCEROL AND KETONE BODY METABOLISM 168115All SZGR 2.0 genes in this pathway
REACTOME TRANSCRIPTIONAL REGULATION OF WHITE ADIPOCYTE DIFFERENTIATION 7253All SZGR 2.0 genes in this pathway
REACTOME SIGNALING BY NOTCH 10364All SZGR 2.0 genes in this pathway
REACTOME SIGNALING BY TGF BETA RECEPTOR COMPLEX 6342All SZGR 2.0 genes in this pathway
HOLLMANN APOPTOSIS VIA CD40 UP 201125All SZGR 2.0 genes in this pathway
GAZDA DIAMOND BLACKFAN ANEMIA ERYTHROID DN 493298All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE LIVE UP 485293All SZGR 2.0 genes in this pathway
HOEBEKE LYMPHOID STEM CELL UP 9564All SZGR 2.0 genes in this pathway
SENESE HDAC3 TARGETS DN 536332All SZGR 2.0 genes in this pathway
KINSEY TARGETS OF EWSR1 FLII FUSION DN 329219All SZGR 2.0 genes in this pathway
ENK UV RESPONSE EPIDERMIS DN 508354All SZGR 2.0 genes in this pathway
SCHEIDEREIT IKK TARGETS 1815All SZGR 2.0 genes in this pathway
MARTIN INTERACT WITH HDAC 4431All SZGR 2.0 genes in this pathway
SCHLOSSER SERUM RESPONSE AUGMENTED BY MYC 10874All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 DN 855609All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 COMMON DN 483336All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK 1442892All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS DN 637377All SZGR 2.0 genes in this pathway
FERREIRA EWINGS SARCOMA UNSTABLE VS STABLE DN 9859All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 48HR DN 428306All SZGR 2.0 genes in this pathway
FLECHNER PBL KIDNEY TRANSPLANT OK VS DONOR UP 151100All SZGR 2.0 genes in this pathway
KLEIN PRIMARY EFFUSION LYMPHOMA UP 5129All SZGR 2.0 genes in this pathway
HSIAO LIVER SPECIFIC GENES 244154All SZGR 2.0 genes in this pathway
THEILGAARD NEUTROPHIL AT SKIN WOUND UP 7752All SZGR 2.0 genes in this pathway
MARTINEZ RESPONSE TO TRABECTEDIN 5032All SZGR 2.0 genes in this pathway
NATSUME RESPONSE TO INTERFERON BETA DN 5233All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP 16911088All SZGR 2.0 genes in this pathway
SESTO RESPONSE TO UV C5 4636All SZGR 2.0 genes in this pathway
SATO SILENCED BY METHYLATION IN PANCREATIC CANCER 1 419273All SZGR 2.0 genes in this pathway
DOUGLAS BMI1 TARGETS UP 566371All SZGR 2.0 genes in this pathway
MITSIADES RESPONSE TO APLIDIN UP 439257All SZGR 2.0 genes in this pathway
HSIAO HOUSEKEEPING GENES 389245All SZGR 2.0 genes in this pathway
MARTENS BOUND BY PML RARA FUSION 456287All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN 19721213All SZGR 2.0 genes in this pathway
BHAT ESR1 TARGETS NOT VIA AKT1 UP 211131All SZGR 2.0 genes in this pathway
BHAT ESR1 TARGETS VIA AKT1 UP 281183All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-106706771A,m8hsa-miR-10aUACCCUGUAGAUCCGAAUUUGUG
hsa-miR-10bUACCCUGUAGAACCGAAUUUGU
miR-124.11691751Ahsa-miR-124aUUAAGGCACGCGGUGAAUGCCA
miR-125/351215221m8hsa-miR-125bbrainUCCCUGAGACCCUAACUUGUGA
hsa-miR-125abrainUCCCUGAGACCCUUUAACCUGUG
miR-1841361431A,m8hsa-miR-184UGGACGGAGAACUGAUAAGGGU
miR-29232238m8hsa-miR-29aSZUAGCACCAUCUGAAAUCGGUU
hsa-miR-29bSZUAGCACCAUUUGAAAUCAGUGUU
hsa-miR-29cSZUAGCACCAUUUGAAAUCGGU
miR-30-5p224230m8hsa-miR-30a-5pUGUAAACAUCCUCGACUGGAAG
hsa-miR-30cbrainUGUAAACAUCCUACACUCUCAGC
hsa-miR-30dSZUGUAAACAUCCCCGACUGGAAG
hsa-miR-30bSZUGUAAACAUCCUACACUCAGCU
hsa-miR-30e-5pUGUAAACAUCCUUGACUGGA
miR-3312172231Ahsa-miR-331brainGCCCCUGGGCCUAUCCUAGAA
miR-9377383m8hsa-miR-9SZUCUUUGGUUAUCUAGCUGUAUGA