Cancer Cell Metabolism Gene Database

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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 TNFRSF21
Basic gene info.Gene symbolTNFRSF21
Gene nametumor necrosis factor receptor superfamily, member 21
SynonymsBM-018|CD358|DR6
CytomapUCSC genome browser: 6p21.1
Genomic locationchr6 :47199267-47277680
Type of geneprotein-coding
RefGenesNM_014452.4,
Ensembl idENSG00000146072
DescriptionTNFR-related death receptor 6death receptor 6tumor necrosis factor receptor superfamily member 21
Modification date20141207
dbXrefs MIM : 605732
HGNC : HGNC
Ensembl : ENSG00000146072
HPRD : 05759
Vega : OTTHUMG00000014796
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TNFRSF21
BioGPS: 27242
Gene Expression Atlas: ENSG00000146072
The Human Protein Atlas: ENSG00000146072
PathwayNCI Pathway Interaction Database: TNFRSF21
KEGG: TNFRSF21
REACTOME: TNFRSF21
ConsensusPathDB
Pathway Commons: TNFRSF21
MetabolismMetaCyc: TNFRSF21
HUMANCyc: TNFRSF21
RegulationEnsembl's Regulation: ENSG00000146072
miRBase: chr6 :47,199,267-47,277,680
TargetScan: NM_014452
cisRED: ENSG00000146072
ContextiHOP: TNFRSF21
cancer metabolism search in PubMed: TNFRSF21
UCL Cancer Institute: TNFRSF21
Assigned class in ccmGDBC

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Phenotypic Information for TNFRSF21(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TNFRSF21
Familial Cancer Database: TNFRSF21
* 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: TNFRSF21
MedGen: TNFRSF21 (Human Medical Genetics with Condition)
ClinVar: TNFRSF21
PhenotypeMGI: TNFRSF21 (International Mouse Phenotyping Consortium)
PhenomicDB: TNFRSF21

Mutations for TNFRSF21
* 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
There's no inter-chromosomal structural variation.
- 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
ovaryTNFRSF21chr64723310747233127TNFRSF21chr64723315747233177
ovaryTNFRSF21chr64725051247250532GPR116chr64688417146884191
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 TNFRSF21 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DB231778RPL131274168962709089627753TNFRSF2127057464725416347277287
BE720121TNFRSF212724464725375247253968MAMLD1240601X149540925149541772

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 # sample1  1 1  1     1  
GAIN (# sample)1  1 1        1  
LOSS (# sample)        1        
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=46)
Stat. for Synonymous SNVs
(# total SNVs=18)
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
chr6:47221018-47221018p.R495C4
chr6:47202494-47202494p.F550F4
chr6:47200581-47200581p.E630K4
chr6:47200703-47200703p.V589G3
chr6:47221138-47221138p.D455N3
chr6:47253992-47253992p.P146S2
chr6:47254004-47254004p.A142T2
chr6:47202423-47202423p.G574V2
chr6:47221041-47221041p.R487T2
chr6:47252127-47252127p.P264S2

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample35 13  3 11 231  195 9
# mutation35 13  3 11 231  175 11
nonsynonymous SNV32 8  2  1 231  94 6
synonymous SNV 3 5  1 1       81 5
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
chr6:47202494p.F550F4
chr6:47200581p.E630Q3
chr6:47253992p.R487T2
chr6:47221138p.P146S2
chr6:47221041p.D455N2
chr6:47200672p.P242S1
chr6:47252065p.D58D1
chr6:47221045p.G574V1
chr6:47253860p.N412S1
chr6:47254313p.S224S1

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 TNFRSF21 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 TNFRSF21

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

APP,B3GNT5,C6orf15,CCDC82,CDH3,CDK2AP1,CORO1C,
FAM171A1,FBXO10,GYLTL1B,IFRD1,MPZL1,MSN,NCK2,
OGFRL1,PTK7,SRPK1,TNFRSF21,UBASH3B,UBXN2A,YEATS2
ADAMTS12,ALDH9A1,CLMP,C17orf51,ENPEP,FAM92A1,GAB2,
IGF1,LARP1,LDHB,MRAS,NTM,TENM4,PDZD2,
PLOD2,PRICKLE2,PXDN,SELENBP1,STAT5B,TLN2,TNFRSF21

ARL14,B3GNT5,CTSE,DHRS9,DUSP5,EMP1,ERRFI1,
EZR,F3,GCNT3,GJB4,GPR110,GPRC5A,LIPH,
LRRC1,MALL,MMP28,MXD1,PPARD,TNFRSF21,TSPAN1
DSC2,EMP1,EPAS1,FLNB,GPR37L1,GPRC5A,HAS3,
LANCL3,MICAL2,MIER3,PPARD,RAPGEF2,RELL1,RHPN2,
RUNDC1,SLC20A2,SLC30A10,TMC7,TMEM2,TNFRSF21,TP53INP2
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 TNFRSF21


There's no related Drug.
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Cross referenced IDs for TNFRSF21
* 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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