Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	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 symbol	NR1D1
	Gene name	nuclear receptor subfamily 1, group D, member 1
	Synonyms	EAR1\|THRA1\|THRAL\|ear-1\|hRev
	Cytomap	UCSC genome browser: 17q11.2
	Genomic location	chr17 :38249036-38256973
	Type of gene	protein-coding
	RefGenes	NM_021724.4,
	Ensembl id	ENSG00000126368
	Description	Rev-ErbAalphaV-erbA-related protein 1nuclear receptor Rev-ErbA-alphanuclear receptor subfamily 1 group D member 1rev-erbA-alpha
	Modification date	20141207
dbXrefs	MIM : 602408
	HGNC : HGNC
	Ensembl : ENSG00000126368
	HPRD : 03873
	Vega : OTTHUMG00000133327
Protein	UniProt: P20393 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NR1D1
	BioGPS: 9572
	Gene Expression Atlas: ENSG00000126368
	The Human Protein Atlas: ENSG00000126368
Pathway	NCI Pathway Interaction Database: NR1D1
	KEGG: NR1D1
	REACTOME: NR1D1
	ConsensusPathDB
	Pathway Commons: NR1D1
Metabolism	MetaCyc: NR1D1
	HUMANCyc: NR1D1
Regulation	Ensembl's Regulation: ENSG00000126368
	miRBase: chr17 :38,249,036-38,256,973
	TargetScan: NM_021724
	cisRED: ENSG00000126368
Context	iHOP: NR1D1
	cancer metabolism search in PubMed: NR1D1
	UCL Cancer Institute: NR1D1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of NR1D1 in cancer cell metabolism	1. 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

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Phenotypic Information for NR1D1(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM	602408; gene.
Orphanet
Disease	KEGG Disease: NR1D1
	MedGen: NR1D1 (Human Medical Genetics with Condition)
	ClinVar: NR1D1
Phenotype	MGI: NR1D1 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	NR1D1	chr17	38249494	38249514		chr20	60544000	60544020

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows NR1D1 related fusion information.

Head Gene

Tail Gene

Accession

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

BE720232

SLC6A15

85305516

85305595

NR1D1

514

38250331

38251900

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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)

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SNV 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

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Somatic 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.

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Top 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 position	Mutation(aa)	Unique sampleID count
chr17:38252720-38252720	p.L194V	2
chr17:38252828-38252828	p.R158G	2
chr17:38249536-38249536	p.?	2
chr17:38251360-38251360	p.N421S	2
chr17:38252961-38252961	p.A148T	2
chr17:38253497-38253497	p.P64L	2
chr17:38250298-38250298	p.S504S	1
chr17:38252302-38252302	p.R215W	1
chr17:38251794-38251794	p.N384S	1
chr17:38253337-38253337	p.K117K	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	2	3		7	2		1					2		1			1	5		6
# mutation	2	3		8	2		1					2		1			1	6		8
nonsynonymous SNV	2	2		6			1					2						4		4
synonymous SNV		1		2	2									1			1	2		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])

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Top 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 Position	Mutation(aa)	Unique sampleID count
chr17:38252961	p.A148T	2
chr17:38253428	p.S504S	1
chr17:38251797	p.S240S	1
chr17:38252225	p.R500H	1
chr17:38253454	p.R211R	1
chr17:38251805	p.T476A	1
chr17:38252312	p.R204H	1
chr17:38253490	p.R448L	1
chr17:38251870	p.R157C	1
chr17:38252334	p.N384T	1

Other 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

Copy 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]

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Gene Expression for NR1D1

Gene 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.

Differential 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))

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CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

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Gene-Gene Network Information

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting Genes (from Pathway Commons)

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

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Pharmacological Information for NR1D1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P20393; -.
Chemistry	ChEMBL	CHEMBL1961783; -.
Chemistry	GuidetoPHARMACOLOGY	596; -.
Organism-specific databases	PharmGKB	PA31748; -.
Organism-specific databases	CTD	9572; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB01356	nuclear receptor subfamily 1, group D, member 1	approved	Lithium

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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