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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SMG6 |
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Phenotypic Information for SMG6(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: SMG6 |
Familial Cancer Database: SMG6 |
* 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 |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: SMG6 |
MedGen: SMG6 (Human Medical Genetics with Condition) | |
ClinVar: SMG6 | |
Phenotype | MGI: SMG6 (International Mouse Phenotyping Consortium) |
PhenomicDB: SMG6 |
Mutations for SMG6 |
* 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 |
- Statistics for Tissue and Mutation type | Top |
- For Inter-chromosomal Variations |
There's no inter-chromosomal structural variation. |
- For Intra-chromosomal Variations |
There's no intra-chromosomal structural variation. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
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) |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SMG6 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 |
DA746032 | ZFP36L1 | 1 | 118 | 14 | 69261839 | 69261956 | SMG6 | 116 | 563 | 17 | 1968369 | 1972227 | |
BP250136 | NPIPB7 | 1 | 382 | 16 | 28548976 | 28550333 | SMG6 | 377 | 592 | 17 | 2057997 | 2058212 | |
BP223879 | SMG6 | 1 | 147 | 17 | 2113443 | 2113589 | DSG2 | 147 | 661 | 18 | 29111160 | 29118801 | |
BE837736 | SMG6 | 1 | 292 | 17 | 2115708 | 2115998 | ITFG2 | 284 | 483 | 12 | 2933402 | 2933601 | |
BF733944 | SMG6 | 14 | 229 | 17 | 2203163 | 2203379 | TNRC6A | 214 | 309 | 16 | 24802394 | 24802489 |
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=89) | (# total SNVs=30) |
(# total SNVs=1) | (# total SNVs=0) |
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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 |
chr17:2203200-2203200 | p.Q283* | 3 |
chr17:2203175-2203175 | p.R291P | 2 |
chr17:2203910-2203910 | p.R46H | 2 |
chr17:2202843-2202843 | p.R402W | 2 |
chr17:2203916-2203916 | p.N44I | 2 |
chr17:2203453-2203453 | p.A198A | 2 |
chr17:2202449-2202449 | p.G533D | 2 |
chr17:2139842-2139842 | p.R938H | 2 |
chr17:2186958-2186958 | p.K803K | 2 |
chr17:2196207-2196207 | p.R739Q | 2 |
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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 | 2 | 1 | 3 | 15 |   |   | 3 |   | 5 |   |   | 7 | 6 | 1 |   | 1 | 7 | 15 | 1 | 11 |
# mutation | 2 | 1 | 3 | 16 |   |   | 3 |   | 5 |   |   | 7 | 6 | 1 |   | 1 | 8 | 16 | 1 | 15 |
nonsynonymous SNV | 1 | 1 | 1 | 13 |   |   | 3 |   | 3 |   |   | 6 | 5 | 1 |   |   | 5 | 8 |   | 14 |
synonymous SNV | 1 |   | 2 | 3 |   |   |   |   | 2 |   |   | 1 | 1 |   |   | 1 | 3 | 8 | 1 | 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 |
chr17:2202843 | p.A613A | 2 |
chr17:2203910 | p.R402W | 2 |
chr17:2202208 | p.R46H | 2 |
chr17:2186922 | p.P40P | 1 |
chr17:2202732 | p.R292W,SMG6 | 1 |
chr17:1964860 | p.L111M,SMG6 | 1 |
chr17:2200581 | p.K697M | 1 |
chr17:2203274 | p.V483V | 1 |
chr17:2076117 | p.T256T | 1 |
chr17:2202345 | p.N31K | 1 |
Other DBs for Point Mutations |
Copy Number for SMG6 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 SMG6 |
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 |
ABR,ANKFY1,CTC1,C17orf85,CAMTA2,CHD3,CTNS, DPH1,KIAA0753,METTL16,MINK1,MNT,NEURL4,SGSM2, SHPK,SMG6,SMYD4,VPS53,WDR81,ZBTB4,ZZEF1 | ALX3,ANKRD11,C22orf46,CEP250,CHD3,SPECC1L,DHX38, EXOC7,STRIP1,GLG1,IP6K1,LTBP3,NUMA1,PRR12, RBM19,SMG6,SUPT6H,TNRC18,UPF1,ZC3H7B,ZNF646 |
AHDC1,AKAP13,ANKFY1,CAMTA2,CTNS,FLII,FXR2, KDM6B,MNT,MPRIP,MYO1C,NCOR1,PAFAH1B1,POLR2A, PRPF8,RABEP1,RAI1,SMG6,WDR81,ZBTB4,ZNF407 | PRRC2B,HECTD4,CHD8,CREBBP,DDX42,DYNC1H1,EP300, EP400,FAM193A,GLG1,HERC2,HUWE1,MED12,MED13L, NCOR2,NUMA1,SMG6,SNRNP200,SUPT6H,TNRC6C,ZNF407 |
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 SMG6 |
There's no related Drug. |
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Cross referenced IDs for SMG6 |
* 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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