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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for TNFSF13 |
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Phenotypic Information for TNFSF13(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: TNFSF13 |
Familial Cancer Database: TNFSF13 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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_MRNA REACTOME_METABOLISM_OF_RNA |
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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows TNFSF13 related fusion information. |
ID | 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 |
BC156811 | TNFSF12 | 28 | 419 | 17 | 7549058 | 7557890 | TNFSF13 | 420 | 1025 | 17 | 7558292 | 7561608 | |
NM_172089 | TNFSF12 | 28 | 419 | 17 | 7549058 | 7557890 | TNFSF13 | 420 | 1864 | 17 | 7558292 | 7561608 |
Other DBs for Structural Variants |
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Copy 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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=7) | (# total SNVs=5) |
(# total SNVs=0) | (# total SNVs=3) |
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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 |
chr17:7464141-7464141 | p.V248V | 2 |
chr17:7462431-7462431 | p.P25P | 2 |
chr17:7462459-7462460 | p.A37fs*88 | 2 |
chr17:7463198-7463198 | p.A125T | 1 |
chr17:7463369-7463369 | p.D130V | 1 |
chr17:7463393-7463394 | p.P140fs*37 | 1 |
chr17:7463398-7463398 | p.P140S | 1 |
chr17:7462439-7462439 | p.S28* | 1 |
chr17:7463440-7463440 | p.G154R | 1 |
chr17:7462449-7462449 | p.L31L | 1 |
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SNV Counts per Each Loci in TCGA data |
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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 |   |   |   |   |   |   | 1 | 1 |   |   |   |   | 1 |   |   |   |   |   |   |   |
# mutation |   |   |   |   |   |   | 1 | 1 |   |   |   |   | 1 |   |   |   |   |   |   |   |
nonsynonymous SNV |   |   |   |   |   |   | 1 | 1 |   |   |   |   |   |   |   |   |   |   |   |   |
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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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 |
chr17:7462433 | p.A26V,TNFSF13 | 1 |
chr17:7462449 | p.L31L,TNFSF13 | 1 |
chr17:7462496 | p.A47V,TNFSF13 | 1 |
Other DBs for Point Mutations |
Copy 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 |
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. |
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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 |
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 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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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 |
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