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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SMG7 |
Basic gene info. | Gene symbol | SMG7 |
Gene name | SMG7 nonsense mediated mRNA decay factor | |
Synonyms | C1orf16|EST1C|SGA56M | |
Cytomap | UCSC genome browser: 1q25 | |
Genomic location | chr1 :183441505-183523328 | |
Type of gene | protein-coding | |
RefGenes | NM_001174061.1, NM_173156.2,NM_201568.2,NM_201569.2,NM_014837.3, | |
Ensembl id | ENSG00000116698 | |
Description | EST1 telomerase component homolog CEST1-like protein Cbreast cancer-associated antigen SGA-56Mever shorter telomeres 1Cprotein SMG7smg-7 homolog, nonsense mediated mRNA decay factor | |
Modification date | 20141207 | |
dbXrefs | MIM : 610964 | |
HGNC : HGNC | ||
Ensembl : ENSG00000116698 | ||
HPRD : 10723 | ||
Vega : OTTHUMG00000035221 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_SMG7 | |
BioGPS: 9887 | ||
Gene Expression Atlas: ENSG00000116698 | ||
The Human Protein Atlas: ENSG00000116698 | ||
Pathway | NCI Pathway Interaction Database: SMG7 | |
KEGG: SMG7 | ||
REACTOME: SMG7 | ||
ConsensusPathDB | ||
Pathway Commons: SMG7 | ||
Metabolism | MetaCyc: SMG7 | |
HUMANCyc: SMG7 | ||
Regulation | Ensembl's Regulation: ENSG00000116698 | |
miRBase: chr1 :183,441,505-183,523,328 | ||
TargetScan: NM_001174061 | ||
cisRED: ENSG00000116698 | ||
Context | iHOP: SMG7 | |
cancer metabolism search in PubMed: SMG7 | ||
UCL Cancer Institute: SMG7 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for SMG7(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: SMG7 |
Familial Cancer Database: SMG7 |
* 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: SMG7 |
MedGen: SMG7 (Human Medical Genetics with Condition) | |
ClinVar: SMG7 | |
Phenotype | MGI: SMG7 (International Mouse Phenotyping Consortium) |
PhenomicDB: SMG7 |
Mutations for SMG7 |
* 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 |
* 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'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
pancreas | SMG7 | chr1 | 183448375 | 183448395 | chr1 | 183425116 | 183425136 | |
pancreas | SMG7 | chr1 | 183448377 | 183448397 | chr1 | 183425116 | 183425136 |
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 SMG7 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 |
BF872191 | SMG7 | 1 | 171 | 1 | 183457369 | 183457540 | HNRNPF | 164 | 302 | 10 | 43885934 | 43886072 | |
AA598525 | SMG7 | 1 | 338 | 1 | 183522990 | 183523326 | SMG7 | 335 | 478 | 1 | 183522874 | 183523017 | |
H80346 | SMG7 | 1 | 29 | 1 | 183463921 | 183463949 | FBXL20 | 13 | 288 | 17 | 37525934 | 37526469 | |
BI014023 | CDK13 | 11 | 313 | 7 | 40042752 | 40043102 | SMG7 | 299 | 508 | 1 | 183512092 | 183512301 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample |   |   |   | 1 |   |   |   |   |   |   | 3 |   |   |   |   |   |   | |||
GAIN (# sample) |   |   |   | 1 |   |   |   |   |   |   | 3 |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
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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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=71) | (# total SNVs=25) |
(# total SNVs=5) | (# 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 |
chr1:183495729-183495729 | p.? | 7 |
chr1:183502837-183502837 | p.C345R | 4 |
chr1:183520210-183520210 | p.S1062L | 3 |
chr1:183515224-183515224 | p.E832Q | 2 |
chr1:183520952-183520952 | p.? | 2 |
chr1:183510179-183510179 | p.R452R | 2 |
chr1:183515267-183515267 | p.M849fs*1 | 2 |
chr1:183498593-183498593 | p.F256F | 2 |
chr1:183515287-183515287 | p.P853S | 2 |
chr1:183498642-183498642 | p.R273* | 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 | 3 | 2 |   | 14 | 3 |   | 2 |   | 2 |   |   | 9 | 10 | 2 |   | 1 | 11 | 2 | 1 | 14 |
# mutation | 4 | 2 |   | 12 | 3 |   | 2 |   | 2 |   |   | 10 | 10 | 2 |   | 1 | 11 | 2 | 1 | 16 |
nonsynonymous SNV | 4 | 1 |   | 9 | 1 |   | 1 |   | 2 |   |   | 9 | 9 | 1 |   | 1 | 9 | 2 | 1 | 12 |
synonymous SNV |   | 1 |   | 3 | 2 |   | 1 |   |   |   |   | 1 | 1 | 1 |   |   | 2 |   |   | 4 |
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 |
chr1:183502837 | p.C303R,SMG7 | 4 |
chr1:183495796 | p.Y778F,SMG7 | 1 |
chr1:183511600 | p.D1003N,SMG7 | 1 |
chr1:183519030 | p.K90K,SMG7 | 1 |
chr1:183502380 | p.E362E,SMG7 | 1 |
chr1:183514220 | p.Q562H,SMG7 | 1 |
chr1:183510187 | p.E790Q,SMG7 | 1 |
chr1:183515372 | p.H1013R,SMG7 | 1 |
chr1:183495814 | p.T92T,SMG7 | 1 |
chr1:183511607 | p.L379I,SMG7 | 1 |
Other DBs for Point Mutations |
Copy Number for SMG7 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 SMG7 |
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 |
AHCTF1,PRRC2C,SPRTN,BROX,SUCO,CAMSAP2,CDC73, CEP350,DHX9,FAM20B,FLVCR1,IPO9,RAB3GAP2,RBBP5, SLC25A44,SMG7,STX6,TADA1,TOR1AIP2,TPR,TROVE2 | ARID2,PRR14L,CNOT1,AGO1,HEATR1,MGA,NF1, RNF111,SMG7,STX17,TNKS,TUG1,ZMYM4,ZKSCAN8, ZNF253,ZNF420,ZNF510,ZNF585A,ZNF616,ZNF623,ZNF81 |
ARHGEF11,ASH1L,PRRC2C,BCL9,CEP350,GON4L,HEATR1, LPGAT1,MTR,NCOA6,POGK,RAB3GAP2,RPRD2,SETDB1, SMG7,STX6,TP53BP2,UBAP2L,UBE2Q1,ZC3H11A,ZNF687 | AKAP13,BIRC6,CDK13,FOXJ3,FOXO3B,GBF1,GOLGB1, IGF2R,KDM2A,NCOR1,NF1,NIPBL,RALGAPB,SMG7, SON,SPEN,TNRC6B,UBN1,UBR4,UPF1,USP9X |
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 SMG7 |
There's no related Drug. |
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Cross referenced IDs for SMG7 |
* 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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