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 TNFSF13
Basic gene info.Gene symbolTNFSF13
Gene nametumor necrosis factor (ligand) superfamily, member 13
SynonymsAPRIL|CD256|TALL-2|TALL2|TRDL-1|ZTNF2
CytomapUCSC genome browser: 17p13.1
Genomic locationchr17 :7461608-7464925
Type of geneprotein-coding
RefGenesNM_001198622.1,
NM_001198623.1,NM_001198624.1,NM_003808.3,NM_172087.2,
NM_172088.2,NR_073490.2,
Ensembl idENSG00000161955
DescriptionTNF- and APOL-related leukocyte expressed ligand 2a proliferation-inducing ligandtumor necrosis factor ligand superfamily member 13tumor necrosis factor-like protein ZTNF2tumor necrosis factor-related death ligand-1
Modification date20141207
dbXrefs MIM : 604472
HGNC : HGNC
Ensembl : ENSG00000161955
Vega : OTTHUMG00000108145
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TNFSF13
BioGPS: 8741
Gene Expression Atlas: ENSG00000161955
The Human Protein Atlas: ENSG00000161955
PathwayNCI Pathway Interaction Database: TNFSF13
KEGG: TNFSF13
REACTOME: TNFSF13
ConsensusPathDB
Pathway Commons: TNFSF13
MetabolismMetaCyc: TNFSF13
HUMANCyc: TNFSF13
RegulationEnsembl's Regulation: ENSG00000161955
miRBase: chr17 :7,461,608-7,464,925
TargetScan: NM_001198622
cisRED: ENSG00000161955
ContextiHOP: TNFSF13
cancer metabolism search in PubMed: TNFSF13
UCL Cancer Institute: TNFSF13
Assigned class in ccmGDBC

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Phenotypic Information for TNFSF13(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TNFSF13
Familial Cancer Database: TNFSF13
* 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_MRNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: TNFSF13
MedGen: TNFSF13 (Human Medical Genetics with Condition)
ClinVar: TNFSF13
PhenotypeMGI: TNFSF13 (International Mouse Phenotyping Consortium)
PhenomicDB: TNFSF13

Mutations for TNFSF13
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows TNFSF13 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BC156811TNFSF12284191775490587557890TNFSF1342010251775582927561608
NM_172089TNFSF12284191775490587557890TNFSF1342018641775582927561608

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
There's no copy number variation information in COSMIC data for this gene.

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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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=7)
Stat. for Synonymous SNVs
(# total SNVs=5)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=3)
There's no deleted 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
chr17:7462431-7462431p.P25P2
chr17:7462459-7462460p.A37fs*882
chr17:7464141-7464141p.V248V2
chr17:7463393-7463394p.P140fs*371
chr17:7463398-7463398p.P140S1
chr17:7462439-7462439p.S28*1
chr17:7463440-7463440p.G154R1
chr17:7462449-7462449p.L31L1
chr17:7463447-7463447p.R156Q1
chr17:7463672-7463672p.L170L1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample      11    1       
# mutation      11    1       
nonsynonymous SNV      11            
synonymous SNV            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
chr17:7462433p.A26V,TNFSF131
chr17:7462449p.L31L,TNFSF131
chr17:7462496p.A47V,TNFSF131

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 TNFSF13 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 TNFSF13

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

KIAA1211L,CAMTA2,CYB5D1,CYB5D2,DLG4,FUCA1,IVD,
LRRC48,MKNK2,MPDU1,MYO1C,NUCB2,PARP3,SLC22A18,
TMEM107,TMEM25,TNFSF13,TNK1,VAMP2,ZBTB4,ZNF18
BAIAP2,SYNE4,CRB3,DNAL4,ELMO3,EPS8L2,FBXW9,
H2AFY2,LOC92659,PAK4,PRKCZ,PRRG2,SCAMP4,SLC35B2,
SPINT2,ST14,STXBP2,SYTL1,TMED3,TMEM125,TNFSF13

ALAS1,C4orf19,CLDN7,CYB5D2,DAPP1,CTDNEP1,LIMA1,
MAP2K4,MED11,MPDU1,MUC1,PDZK1IP1,PHF23,PIGR,
RILP,SLC37A1,TMEM102,TMEM92,TNFSF13,TNK1,TRIM16
ALG1,BIK,DDOST,DUS1L,FKBP11,HM13,LRG1,
MTX1,PDZK1IP1,RPN1,SLC35A2,SLC38A5,SORD,SYNGR2,
TMC6,TMED9,TNFSF13,TRABD,UBE2S,WDR46,ZDHHC16
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 TNFSF13


There's no related Drug.
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Cross referenced IDs for TNFSF13
* 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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