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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for TIMM50 |
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Phenotypic Information for TIMM50(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: TIMM50 |
Familial Cancer Database: TIMM50 |
* 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_PROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: TIMM50 |
MedGen: TIMM50 (Human Medical Genetics with Condition) | |
ClinVar: TIMM50 | |
Phenotype | MGI: TIMM50 (International Mouse Phenotyping Consortium) |
PhenomicDB: TIMM50 |
Mutations for TIMM50 |
* 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 |
pancreas | TIMM50 | chr19 | 39975450 | 39975470 | chr19 | 36824376 | 36824396 |
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 TIMM50 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 |
BF763267 | AGRN | 75 | 94 | 1 | 978392 | 978411 | TIMM50 | 86 | 297 | 19 | 39978835 | 39980445 |
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=31) | (# total SNVs=9) |
(# total SNVs=2) | (# 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 |
chr19:39971368-39971368 | p.D62H | 3 |
chr19:39971574-39971574 | p.A130A | 2 |
chr19:39971367-39971367 | p.P61P | 2 |
chr19:39978708-39978708 | p.S338L | 2 |
chr19:39976916-39976916 | p.T297T | 2 |
chr19:39971440-39971440 | p.P86T | 1 |
chr19:39978811-39978811 | p.G372G | 1 |
chr19:39976238-39976238 | p.R226K | 1 |
chr19:39980431-39980431 | p.R448C | 1 |
chr19:39971205-39971205 | p.L7L | 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 |   | 5 |   |   | 3 |   |   |   |   | 2 | 1 | 2 |   |   | 8 | 4 |   | 5 |
# mutation |   | 3 |   | 6 |   |   | 3 |   |   |   |   | 2 | 1 | 2 |   |   | 8 | 4 |   | 5 |
nonsynonymous SNV |   | 2 |   | 6 |   |   | 2 |   |   |   |   | 2 | 1 |   |   |   | 5 | 3 |   | 3 |
synonymous SNV |   | 1 |   |   |   |   | 1 |   |   |   |   |   |   | 2 |   |   | 3 | 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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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 |
chr19:39976208 | p.P245L | 1 |
chr19:39978708 | p.S433F | 1 |
chr19:39971205 | p.V254I | 1 |
chr19:39980432 | p.T446P | 1 |
chr19:39976330 | p.L7L | 1 |
chr19:39978732 | p.L257P | 1 |
chr19:39971230 | p.R448H | 1 |
chr19:39980444 | p.R16C | 1 |
chr19:39976337 | p.P289L | 1 |
chr19:39978750 | p.R452H | 1 |
Other DBs for Point Mutations |
Copy Number for TIMM50 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 TIMM50 |
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 |
COX6B1,EID2,EIF3K,FBL,LIN37,LRFN1,MRPS12, NFKBIB,PAF1,POLR2I,PSMC4,PSMD8,RBM42,RPS16, SARS2,SIRT2,SUPT5H,TBCB,TIMM50,TMEM147,YIF1B | AKT1S1,ANAPC11,ATP5I,CLPP,COX8A,FAM195A,MRPL12, MRPL2,MRPL38,MRPL41,NDUFA13,NDUFA2,NDUFB11,NDUFB7, NDUFB8,NDUFS8,PHPT1,PRDX2,PAM16,TIMM50,UQCR11 |
BCL2L12,COX6B1,EIF3K,EXOSC5,FBL,GADD45GIP1,GEMIN7, ICT1,LSM7,MRPL11,MRPS12,NME1,PDCD2L,POLR2I, PRMT1,PSMD8,RPS16,RUVBL2,SDHAF1,SNRPD2,TIMM50 | ADSL,BANF1,BOLA3,EBNA1BP2,GADD45GIP1,MRPL11,MRPL36, MRPS15,MRTO4,NAA10,NHP2,NUTF2,NXT1,POLE3, PPIL1,PRMT1,RABEPK,SNRPB,STOML2,TIMM44,TIMM50 |
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 TIMM50 |
There's no related Drug. |
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Cross referenced IDs for TIMM50 |
* 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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