Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for NR1D1
Basic gene info.Gene symbolNR1D1
Gene namenuclear receptor subfamily 1, group D, member 1
SynonymsEAR1|THRA1|THRAL|ear-1|hRev
CytomapUCSC genome browser: 17q11.2
Genomic locationchr17 :38249036-38256973
Type of geneprotein-coding
RefGenesNM_021724.4,
Ensembl idENSG00000126368
DescriptionRev-ErbAalphaV-erbA-related protein 1nuclear receptor Rev-ErbA-alphanuclear receptor subfamily 1 group D member 1rev-erbA-alpha
Modification date20141207
dbXrefs MIM : 602408
HGNC : HGNC
Ensembl : ENSG00000126368
HPRD : 03873
Vega : OTTHUMG00000133327
ProteinUniProt: P20393
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NR1D1
BioGPS: 9572
Gene Expression Atlas: ENSG00000126368
The Human Protein Atlas: ENSG00000126368
PathwayNCI Pathway Interaction Database: NR1D1
KEGG: NR1D1
REACTOME: NR1D1
ConsensusPathDB
Pathway Commons: NR1D1
MetabolismMetaCyc: NR1D1
HUMANCyc: NR1D1
RegulationEnsembl's Regulation: ENSG00000126368
miRBase: chr17 :38,249,036-38,256,973
TargetScan: NM_021724
cisRED: ENSG00000126368
ContextiHOP: NR1D1
cancer metabolism search in PubMed: NR1D1
UCL Cancer Institute: NR1D1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of NR1D1 in cancer cell metabolism1. Kourtidis A, Jain R, Carkner RD, Eifert C, Brosnan MJ, et al. (2010) An RNA interference screen identifies metabolic regulators NR1D1 and PBP as novel survival factors for breast cancer cells with the ERBB2 signature. Cancer research 70: 1783-1792. go to article

Top
Phenotypic Information for NR1D1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NR1D1
Familial Cancer Database: NR1D1
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 602408; gene.
Orphanet
DiseaseKEGG Disease: NR1D1
MedGen: NR1D1 (Human Medical Genetics with Condition)
ClinVar: NR1D1
PhenotypeMGI: NR1D1 (International Mouse Phenotyping Consortium)
PhenomicDB: NR1D1

Mutations for NR1D1
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasNR1D1chr173824949438249514chr206054400060544020
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows NR1D1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE720232SLC6A15785128530551685305595NR1D180514173825033138251900

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample4  1          1  
GAIN (# sample)4  1          1  
LOSS (# sample)                 
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

Top
check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=2

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=32)
Stat. for Synonymous SNVs
(# total SNVs=18)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

Top
check002.gifTop 10 SNVs Having the Most Samples in COSMIC data
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.
GRCh37 positionMutation(aa)Unique sampleID count
chr17:38252720-38252720p.L194V2
chr17:38252828-38252828p.R158G2
chr17:38249536-38249536p.?2
chr17:38252961-38252961p.A148T2
chr17:38251360-38251360p.N421S2
chr17:38253497-38253497p.P64L2
chr17:38253425-38253425p.S88L1
chr17:38251797-38251797p.S383N1
chr17:38256317-38256317p.G11S1
chr17:38249430-38249430p.R584L1

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample23 72 1    2 1  15 6
# mutation23 82 1    2 1  16 8
nonsynonymous SNV22 6  1    2     4 4
synonymous SNV 1 22        1  12 4
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

Top
check002.gifTop 10 SNVs Having the Most Samples in TCGA data
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.
Genomic PositionMutation(aa)Unique sampleID count
chr17:38252961p.A148T2
chr17:38251980p.R500H1
chr17:38252962p.R211R1
chr17:38250298p.T476A1
chr17:38252038p.R204H1
chr17:38253028p.R448L1
chr17:38250311p.R157C1
chr17:38252039p.N384T1
chr17:38253335p.S383N1
chr17:38251196p.H147H1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for NR1D1 in TCGA
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

Top
Gene Expression for NR1D1

check002.gifGene Expression in Cancer Cell-lines (CCLE)
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

check002.gifDifferential Gene Expression in Primary Tumors (TCGA)
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
Gene-Gene Network Information
check002.gifCo-Expressed gene's network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

APOA5,APOH,CASC3,CCL15,CDC6,CYP2E1,DBP,
LEAP2,LOC90110,MED24,MSL1,MT1F,NR0B2,NR1D1,
ORMDL3,PSMD3,RAPGEFL1,RARA,TEF,THRA,WIPF2
ATP5J,BLCAP,TIMM21,CIART,COG1,DBP,EGFLAM,
FOXJ2,HLF,KCTD8,KLHL21,MKKS,MRPL46,NR1D1,
NR1D2,PER3,RWDD2B,SCMH1,SLC25A23,TEF,TMIE

MIEN1,CASC3,ERBB2,GRB7,MED24,MSL1,NR1D1,
ORMDL3,PGAP3,PPP1R1B,PSMD3,RAPGEFL1,RARA,SNX32,
TCAP,THRA,TIAF1,TUBG2,UNC93B1,USP35,WIPF2
AP2M1,SKIDA1,CIART,CCDC136,CDC42EP4,ESYT1,FNDC1,
FREM1,H19,ILDR2,KIF26B,KRT17,NOS1,NOX4,
NR1D1,NR1D2,PER3,SCUBE3,SMYD1,TEF,THRA
check002.gifCo-Expressed gene's Protein-protein interaction Network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for NR1D1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P20393; -.
ChemistryChEMBL CHEMBL1961783; -.
ChemistryGuidetoPHARMACOLOGY 596; -.
Organism-specific databasesPharmGKB PA31748; -.
Organism-specific databasesCTD 9572; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01356nuclear receptor subfamily 1, group D, member 1approvedLithium


Top
Cross referenced IDs for NR1D1
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas