Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 NRF1
Basic gene info.Gene symbolNRF1
Gene namenuclear respiratory factor 1
SynonymsALPHA-PAL
CytomapUCSC genome browser: 7q32
Genomic locationchr7 :129251554-129396922
Type of geneprotein-coding
RefGenesNM_001040110.1,
NM_001293163.1,NM_001293164.1,NM_005011.4,
Ensembl idENSG00000106459
Descriptionalpha palindromic-binding protein
Modification date20141207
dbXrefs MIM : 600879
HGNC : HGNC
Ensembl : ENSG00000106459
HPRD : 02930
Vega : OTTHUMG00000143736
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NRF1
BioGPS: 4899
Gene Expression Atlas: ENSG00000106459
The Human Protein Atlas: ENSG00000106459
PathwayNCI Pathway Interaction Database: NRF1
KEGG: NRF1
REACTOME: NRF1
ConsensusPathDB
Pathway Commons: NRF1
MetabolismMetaCyc: NRF1
HUMANCyc: NRF1
RegulationEnsembl's Regulation: ENSG00000106459
miRBase: chr7 :129,251,554-129,396,922
TargetScan: NM_001040110
cisRED: ENSG00000106459
ContextiHOP: NRF1
cancer metabolism search in PubMed: NRF1
UCL Cancer Institute: NRF1
Assigned class in ccmGDBC

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Phenotypic Information for NRF1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NRF1
Familial Cancer Database: NRF1
* 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
Orphanet
DiseaseKEGG Disease: NRF1
MedGen: NRF1 (Human Medical Genetics with Condition)
ClinVar: NRF1
PhenotypeMGI: NRF1 (International Mouse Phenotyping Consortium)
PhenomicDB: NRF1

Mutations for NRF1
* 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
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
prostateNRF1chr7129390737129390737chr7155389558155389558
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 NRF1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BC006380NRF1214097129351313129367207EIF4A140715741774784367482036
AA503463NRF18737129377030129377095NRF1682657129376917129377114
CV341784UBE2D335904103717295103717350NRF1876537129269870129270436

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

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample11      3 2  1   
GAIN (# sample)11      3 2  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)

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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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=35)
Stat. for Synonymous SNVs
(# total SNVs=13)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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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
chr7:129317479-129317479p.R116*3
chr7:129297332-129297332p.S47S3
chr7:129357178-129357178p.E395E3
chr7:129367082-129367082p.E409K2
chr7:129351322-129351322p.T324M2
chr7:129317486-129317486p.T118M2
chr7:129357140-129357140p.A383T2
chr7:129297219-129297219p.E10K1
chr7:129350377-129350377p.F310S1
chr7:129349050-129349050p.R248S1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample12152 3 1 16 1  48 5
# mutation12152 3 1 19 1  48 6
nonsynonymous SNV 1141 3 1 15 1  46 5
synonymous SNV11 11      4     2 1
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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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
chr7:129367082p.E248K,NRF13
chr7:129357144p.T118M,NRF12
chr7:129317486p.S223L,NRF12
chr7:129297219p.A63T,NRF11
chr7:129348924p.T163M,NRF11
chr7:129351322p.S326S,NRF11
chr7:129297253p.A72V,NRF11
chr7:129367163p.A165A,NRF11
chr7:129348982p.E341Q,NRF11
chr7:129351329p.R113W,NRF11

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 NRF1 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 NRF1

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))
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check002.gifCNV 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
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

DDX39B,CLDN15,CROCCP2,DGCR8,EGFL8,GIGYF1,ING5,
KRBA1,LOC390595,MAP2K7,NRF1,POLR2J4,PRKRIP1,SAFB,
CLASRP,SFSWAP,WASH7P,WDR27,ZNF212,ZNF767P,ZNF862
ACTR5,BRD1,BZRAP1,CHDH,DVL2,GEMIN4,HAUS5,
LIMK2,NRF1,POLDIP3,RIPK4,SART3,SFSWAP,SH2D3A,
UNK,WDR6,XPC,ZNF202,ZNF263,ZNF346,ZSCAN25

ASXL1,LINC01000,GIGYF1,GMEB2,ILF3,INE1,LOC100129637,
LOC349114,LY6G5B,NRF1,PASK,PLCG1,RBM33,SFSWAP,
SNORA71E,TJAP1,UCKL1-AS1,ZMIZ2,ZNF212,ZNF335,ZSCAN25
ARFGAP2,CEP131,BAP1,CIZ1,DVL2,EHMT2,ERCC2,
FKBP9,H1FX,IFT122,IFT140,KLHL26,MKL1,NRF1,
PATZ1,PDE4A,PLEKHM2,SF3A2,UBE2O,XAB2,ZNF777
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

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check002.gifInteracting 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 NRF1


There's no related Drug.
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Cross referenced IDs for NRF1
* 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



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