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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for TM7SF2 |
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Phenotypic Information for TM7SF2(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: TM7SF2 |
Familial Cancer Database: TM7SF2 |
* This gene is included in those cancer gene databases. |
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 |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: TM7SF2 |
MedGen: TM7SF2 (Human Medical Genetics with Condition) | |
ClinVar: TM7SF2 | |
Phenotype | MGI: TM7SF2 (International Mouse Phenotyping Consortium) |
PhenomicDB: TM7SF2 |
Mutations for TM7SF2 |
* 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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There's no structural variation information in COSMIC data for this gene. |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows TM7SF2 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 |
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There's no copy number variation information in COSMIC data for this gene. |
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Stat. for Non-Synonymous SNVs (# total SNVs=22) | (# total SNVs=12) |
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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 |
chr11:64880090-64880090 | p.P52P | 4 |
chr11:64882275-64882275 | p.L232F | 2 |
chr11:64882420-64882420 | p.D253D | 2 |
chr11:64882953-64882953 | p.E327K | 2 |
chr11:64882979-64882979 | p.R335R | 2 |
chr11:64883491-64883491 | p.R408P | 2 |
chr11:64883379-64883379 | p.L371L | 1 |
chr11:64880874-64880874 | p.N165fs*45 | 1 |
chr11:64882807-64882807 | p.R305L | 1 |
chr11:64883385-64883385 | p.Y373H | 1 |
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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 | 2 | 1 |   | 3 | 1 |   | 2 |   |   |   |   | 5 | 2 | 1 |   | 1 | 5 | 2 |   | 3 |
# mutation | 2 | 1 |   | 3 | 1 |   | 2 |   |   |   |   | 7 | 3 | 1 |   | 1 | 5 | 2 |   | 4 |
nonsynonymous SNV | 1 |   |   | 1 |   |   | 1 |   |   |   |   | 5 | 2 | 1 |   | 1 | 3 | 1 |   | 2 |
synonymous SNV | 1 | 1 |   | 2 | 1 |   | 1 |   |   |   |   | 2 | 1 |   |   |   | 2 | 1 |   | 2 |
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 |
chr11:64882420 | p.D253D,TM7SF2 | 2 |
chr11:64880871 | p.A305V,TM7SF2 | 1 |
chr11:64882440 | p.P169L,TM7SF2 | 1 |
chr11:64883418 | p.R320R,TM7SF2 | 1 |
chr11:64880969 | p.P181H,TM7SF2 | 1 |
chr11:64882447 | p.G326A,TM7SF2 | 1 |
chr11:64883423 | p.P196P,TM7SF2 | 1 |
chr11:64881005 | p.L344L,TM7SF2 | 1 |
chr11:64882533 | p.I199I,TM7SF2 | 1 |
chr11:64883439 | p.A354T,TM7SF2 | 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 TM7SF2 |
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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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BSCL2,LBHD1___C11orf98,UQCC3,C1orf105,CARD18,COX8A,CRIP1, CYP2F1,DCXR,FAU,KRT79,METRN,MRPL49,NME4, PNPLA1,PSAPL1,SAC3D1,SYVN1,TM7SF2,TRPT1,ZNHIT2 | ADH1A,ADH1B,ALDH1L1,ANKRD53,ASS1,APMAP,CIDEA, ECHDC3,HADH,HRSP12,MLX,MLXIPL,MOCS1,ORMDL3, PC,PLA2G16,PMM1,SHMT1,TM7SF2,TMEM120A,TWIST1 |
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ARL2,BANF1,C14orf1,ACTL10,CCS,COA4,DCXR, DHCR7,FAM86C1,FAU,MEN1,MFSD3,NAP1L4,NME4, PGAP2,PPFIA3,PPP1R14B,TAF10,TM7SF2,TRMT61A,TUT1 | C20orf141,NCOR1P1,CLEC4G,CYP51A1,GPX5,IER5L,KPRP, LCE2C,MEPE,CHODL-AS1,OR2D2,PCSK9,PGLYRP3,PTGER1, MSMO1,SEL1L2,SNORA79,SPATS1,TM7SF2,TRIM6-TRIM34,ZSWIM2 |
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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 TM7SF2 |
There's no related Drug. |
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Cross referenced IDs for TM7SF2 |
* 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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