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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for TNFRSF21 |
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Phenotypic Information for TNFRSF21(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: TNFRSF21 |
Familial Cancer Database: TNFRSF21 |
* 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/ |
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REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
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. |
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- Statistics for Tissue and Mutation type | Top |
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- 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'. |
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Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | TNFRSF21 | chr6 | 47233107 | 47233127 | TNFRSF21 | chr6 | 47233157 | 47233177 |
ovary | TNFRSF21 | chr6 | 47250512 | 47250532 | GPR116 | chr6 | 46884171 | 46884191 |
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) |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows TNFRSF21 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 |
DB231778 | RPL13 | 1 | 274 | 16 | 89627090 | 89627753 | TNFRSF21 | 270 | 574 | 6 | 47254163 | 47277287 | |
BE720121 | TNFRSF21 | 27 | 244 | 6 | 47253752 | 47253968 | MAMLD1 | 240 | 601 | X | 149540925 | 149541772 |
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Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample | 1 |   |   | 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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Stat. for Non-Synonymous SNVs (# total SNVs=46) | (# total SNVs=18) |
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(# total SNVs=1) | (# total SNVs=0) |
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* 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 |
chr6:47202494-47202494 | p.F550F | 4 |
chr6:47200581-47200581 | p.E630K | 4 |
chr6:47221018-47221018 | p.R495C | 4 |
chr6:47200703-47200703 | p.V589G | 3 |
chr6:47221138-47221138 | p.D455N | 3 |
chr6:47252127-47252127 | p.P264S | 2 |
chr6:47253756-47253756 | p.S224S | 2 |
chr6:47202528-47202528 | p.E539A | 2 |
chr6:47253992-47253992 | p.P146S | 2 |
chr6:47254004-47254004 | p.A142T | 2 |
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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 | 3 | 5 |   | 13 |   |   | 3 |   | 1 | 1 |   | 2 | 3 | 1 |   |   | 19 | 5 |   | 9 |
# mutation | 3 | 5 |   | 13 |   |   | 3 |   | 1 | 1 |   | 2 | 3 | 1 |   |   | 17 | 5 |   | 11 |
nonsynonymous SNV | 3 | 2 |   | 8 |   |   | 2 |   |   | 1 |   | 2 | 3 | 1 |   |   | 9 | 4 |   | 6 |
synonymous SNV |   | 3 |   | 5 |   |   | 1 |   | 1 |   |   |   |   |   |   |   | 8 | 1 |   | 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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* 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 |
chr6:47202494 | p.F550F | 4 |
chr6:47200581 | p.E630Q | 3 |
chr6:47221041 | p.P146S | 2 |
chr6:47253992 | p.D455N | 2 |
chr6:47221138 | p.R487T | 2 |
chr6:47202544 | p.L644M | 1 |
chr6:47253785 | p.R486R | 1 |
chr6:47221154 | p.P327A | 1 |
chr6:47254171 | p.T190A | 1 |
chr6:47200576 | p.I631I | 1 |
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* 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. |
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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 |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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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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 |
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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 |
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* 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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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 |
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