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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for MCTS1 |
Basic gene info. | Gene symbol | MCTS1 |
Gene name | malignant T cell amplified sequence 1 | |
Synonyms | MCT-1|MCT1 | |
Cytomap | UCSC genome browser: Xq24 | |
Genomic location | chrX :119737743-119755016 | |
Type of gene | protein-coding | |
RefGenes | NM_001137554.1, NM_014060.2, | |
Ensembl id | ENSG00000232119 | |
Description | malignant T-cell-amplified sequence 1multiple copies T-cell malignancies | |
Modification date | 20141207 | |
dbXrefs | MIM : 300587 | |
HGNC : HGNC | ||
HPRD : 06634 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_MCTS1 | |
BioGPS: 28985 | ||
Gene Expression Atlas: ENSG00000232119 | ||
The Human Protein Atlas: ENSG00000232119 | ||
Pathway | NCI Pathway Interaction Database: MCTS1 | |
KEGG: MCTS1 | ||
REACTOME: MCTS1 | ||
ConsensusPathDB | ||
Pathway Commons: MCTS1 | ||
Metabolism | MetaCyc: MCTS1 | |
HUMANCyc: MCTS1 | ||
Regulation | Ensembl's Regulation: ENSG00000232119 | |
miRBase: chrX :119,737,743-119,755,016 | ||
TargetScan: NM_001137554 | ||
cisRED: ENSG00000232119 | ||
Context | iHOP: MCTS1 | |
cancer metabolism search in PubMed: MCTS1 | ||
UCL Cancer Institute: MCTS1 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for MCTS1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: MCTS1 |
Familial Cancer Database: MCTS1 |
* 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 | |
Nat Rev Drug Discovery, 2013, 12: 829, doi: 10.1038/nrd4145 |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: MCTS1 |
MedGen: MCTS1 (Human Medical Genetics with Condition) | |
ClinVar: MCTS1 | |
Phenotype | MGI: MCTS1 (International Mouse Phenotyping Consortium) |
PhenomicDB: MCTS1 |
Mutations for MCTS1 |
* 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 MCTS1 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 |
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=22) | (# total SNVs=3) |
(# 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 |
chr23:119739328-119739328 | p.K26N | 2 |
chr23:119739274-119739274 | p.K8N | 2 |
chr23:119739938-119739938 | p.E57K | 1 |
chr23:119742212-119742212 | p.V132A | 1 |
chr23:119739953-119739953 | p.L62I | 1 |
chr23:119742219-119742219 | p.? | 1 |
chr23:119739341-119739341 | p.E31K | 1 |
chr23:119739979-119739979 | p.F70L | 1 |
chr23:119744919-119744919 | p.M150I | 1 |
chr23:119739354-119739354 | p.G35D | 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 | 2 | 1 |   | 2 |   |   | 1 |   | 2 |   |   | 3 | 1 | 1 |   |   |   | 2 |   | 6 |
# mutation | 2 | 1 |   | 2 |   |   | 1 |   | 2 |   |   | 3 | 1 | 1 |   |   |   | 2 |   | 6 |
nonsynonymous SNV | 2 | 1 |   | 2 |   |   | 1 |   | 2 |   |   | 2 | 1 | 1 |   |   |   | 1 |   | 5 |
synonymous SNV |   |   |   |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   | 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 |
chrX:119742118 | p.G2D | 1 |
chrX:119738719 | p.V133A,MCTS1 | 1 |
chrX:119742128 | p.G4E | 1 |
chrX:119739274 | p.M151I,MCTS1 | 1 |
chrX:119742168 | p.K9N,MCTS1 | 1 |
chrX:119739328 | p.G164D,MCTS1 | 1 |
chrX:119742191 | p.K27N,MCTS1 | 1 |
chrX:119739341 | p.L171F,MCTS1 | 1 |
chrX:119742205 | p.E32K,MCTS1 | 1 |
chrX:119739370 | p.L175L,MCTS1 | 1 |
Other DBs for Point Mutations |
Copy Number for MCTS1 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 MCTS1 |
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 |
AIFM1,ATP5J,BCAP31,C1GALT1C1,CETN2,COX7B,EMD, MCTS1,NDUFA1,NDUFAB1,NKAP,NSDHL,POMP,PSMA2, PSMD10,RBMX2,RNF113A,RPA3,SLC25A14,SLC25A5,UBE2A | BET1,TMEM251,TEFM,METTL23,C18orf32,TMEM243,COMMD6, DUT,FAM200B,HMGB1,HSPB11,LSM5,MCTS1,MED7, PHF11,PIGB,PSMD10,PSMG2,RPP30,SEC22A,SEP15 |
C1GALT1C1,CETN2,CXorf40A,HDAC8,MCTS1,MORF4L2,CMC4, NKAP,NKRF,NSDHL,PDZD11,PGRMC1,PSMD10,RBMX2, RNF113A,SLC25A14,TIMM8A,UBE2A,UTP14A,VBP1,VMA21 | ATG3,LBHD1___C11orf98,C1GALT1C1,TMA7,CHCHD1,CISD2,DPM1, FKBP3,LSM6,MCTS1,MRPL42,OSTC,PSMA5,PSMC6, PTS,SCFD1,SNRPG,TOMM5,UCHL3,YWHAE,ZC3H15 |
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 MCTS1 |
There's no related Drug. |
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Cross referenced IDs for MCTS1 |
* 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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