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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for MTM1 |
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Phenotypic Information for MTM1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: MTM1 |
Familial Cancer Database: MTM1 |
* 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/ |
Metabolic Pathway Description | |
REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_PI_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: MTM1 |
MedGen: MTM1 (Human Medical Genetics with Condition) | |
ClinVar: MTM1 | |
Phenotype | MGI: MTM1 (International Mouse Phenotyping Consortium) |
PhenomicDB: MTM1 |
Mutations for MTM1 |
* 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 MTM1 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 |
AU125262 | MTM1 | 1 | 74 | X | 149840337 | 149840410 | EMG1 | 73 | 781 | 12 | 7090246 | 7125842 | |
AA506682 | MTM1 | 8 | 212 | X | 149841153 | 149841357 | MTM1 | 208 | 285 | X | 149841310 | 149841387 |
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=80) | (# total SNVs=10) |
(# 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 |
chr23:149809883-149809883 | p.R224* | 3 |
chr23:149814235-149814235 | p.R253Q | 3 |
chr23:149831928-149831928 | p.S497Y | 2 |
chr23:149807437-149807437 | p.E156K | 2 |
chr23:149814343-149814343 | p.K289T | 2 |
chr23:149767149-149767149 | p.T77M | 2 |
chr23:149809889-149809889 | p.P226S | 2 |
chr23:149814211-149814211 | p.P245R | 2 |
chr23:149828946-149828946 | p.R486* | 2 |
chr23:149787524-149787524 | p.L119P | 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 | 3 | 7 |   | 8 | 2 |   |   | 1 |   |   |   | 7 | 2 | 1 |   |   | 6 | 1 | 1 | 12 |
# mutation | 3 | 7 |   | 8 | 2 |   |   | 1 |   |   |   | 7 | 2 | 1 |   |   | 6 | 1 | 1 | 13 |
nonsynonymous SNV | 3 | 7 |   | 7 | 2 |   |   | 1 |   |   |   | 6 | 2 | 1 |   |   | 6 | 1 | 1 | 12 |
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:149814235 | p.R253Q | 3 |
chrX:149809819 | p.E156K | 2 |
chrX:149809889 | p.L202F | 2 |
chrX:149807437 | p.T77M | 2 |
chrX:149767149 | p.P226S | 2 |
chrX:149839986 | p.L144P | 1 |
chrX:149814303 | p.S272Y | 1 |
chrX:149787533 | p.W534L | 1 |
chrX:149831928 | p.I276V | 1 |
chrX:149809827 | p.I539V | 1 |
Other DBs for Point Mutations |
Copy Number for MTM1 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 MTM1 |
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 |
APOOL,BIRC6,C9orf41,CAB39,CUL4B,DDX3X,FAM199X, FMR1,KDM6A,LOC284441,MAP3K2,MMGT1,MOB1A,MTM1, MTMR1,PIKFYVE,STAG2,USP9X,VAMP7,WDR44,XIAP | ABHD13,ACBD3,ATF1,BIRC2,TRAPPC13,MAGT1,MARCH7, MFN1,MTM1,MTMR6,MYNN,NAPG,NEDD1,STXBP3, TBK1,TWISTNB,UBXN4,UTP15,VEZF1,YTHDC2,ZNF800 |
APOOL,ATP7A,BRWD3,CHM,CUL4B,CXorf56,ELF4, FAM199X,GNL3L,HERC3,MMGT1,MTM1,MTMR1,OCRL, RPS6KA6,SNX12,STAG2,UBQLN2,XIAP,YIPF6,ZNF41 | ACVR1B,BCAS1,CAPN5,CLMN,EIF2AK3,ENDOD1,FGFR3, GALNT12,IRF6,ITM2C,MCTP2,MTM1,NR3C2,PARM1, PSD3,SCNN1A,SLC4A4,SPIRE2,STYK1,SYTL2,TMEM63B |
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 MTM1 |
There's no related Drug. |
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Cross referenced IDs for MTM1 |
* 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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