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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for TIMM13 |
Basic gene info. | Gene symbol | TIMM13 |
Gene name | translocase of inner mitochondrial membrane 13 homolog (yeast) | |
Synonyms | TIM13|TIM13B|TIMM13A|TIMM13B|ppv1 | |
Cytomap | UCSC genome browser: 19p13.3 | |
Genomic location | chr19 :2425621-2427875 | |
Type of gene | protein-coding | |
RefGenes | NM_012458.3, | |
Ensembl id | ENSG00000099800 | |
Description | mitochondrial import inner membrane translocase subunit Tim13mitochondrial import inner membrane translocase subunit Tim13B | |
Modification date | 20141207 | |
dbXrefs | MIM : 607383 | |
HGNC : HGNC | ||
Ensembl : ENSG00000099800 | ||
HPRD : 09573 | ||
Vega : OTTHUMG00000180432 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_TIMM13 | |
BioGPS: 26517 | ||
Gene Expression Atlas: ENSG00000099800 | ||
The Human Protein Atlas: ENSG00000099800 | ||
Pathway | NCI Pathway Interaction Database: TIMM13 | |
KEGG: TIMM13 | ||
REACTOME: TIMM13 | ||
ConsensusPathDB | ||
Pathway Commons: TIMM13 | ||
Metabolism | MetaCyc: TIMM13 | |
HUMANCyc: TIMM13 | ||
Regulation | Ensembl's Regulation: ENSG00000099800 | |
miRBase: chr19 :2,425,621-2,427,875 | ||
TargetScan: NM_012458 | ||
cisRED: ENSG00000099800 | ||
Context | iHOP: TIMM13 | |
cancer metabolism search in PubMed: TIMM13 | ||
UCL Cancer Institute: TIMM13 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for TIMM13(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: TIMM13 |
Familial Cancer Database: TIMM13 |
* 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: TIMM13 |
MedGen: TIMM13 (Human Medical Genetics with Condition) | |
ClinVar: TIMM13 | |
Phenotype | MGI: TIMM13 (International Mouse Phenotyping Consortium) |
PhenomicDB: TIMM13 |
Mutations for TIMM13 |
* 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 TIMM13 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 |
CN308207 | TIMM13 | 1 | 317 | 19 | 2426921 | 2427534 | BAIAP2 | 307 | 331 | 17 | 79064989 | 79065013 |
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=4) | (# total SNVs=1) |
(# total SNVs=0) | (# 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 |
chr19:2427266-2427266 | p.D59D | 3 |
chr19:2427514-2427514 | p.G6G | 2 |
chr19:2426965-2426965 | p.R90L | 1 |
chr19:2426974-2426974 | p.R87L | 1 |
chr19:2427027-2427027 | p.C69* | 1 |
chr19:2427447-2427447 | p.Q29K | 1 |
chr19:2427462-2427462 | p.E24K | 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 |   | 1 |   |   |   |   | 2 |   |   |   |   |   |   |   |   |   |   |   |   | 2 |
# mutation |   | 1 |   |   |   |   | 2 |   |   |   |   |   |   |   |   |   |   |   |   | 2 |
nonsynonymous SNV |   | 1 |   |   |   |   | 2 |   |   |   |   |   |   |   |   |   |   |   |   | 2 |
synonymous SNV |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
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 |
chr19:2426965 | p.R90L | 1 |
chr19:2426974 | p.R87L | 1 |
chr19:2427036 | p.I66M | 1 |
chr19:2427447 | p.Q29K | 1 |
chr19:2427462 | p.E24K | 1 |
Other DBs for Point Mutations |
Copy Number for TIMM13 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 TIMM13 |
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 |
ATP5D,C19orf24,C19orf70,DOHH,HDGFRP2,LSM7,MAP2K2, MBD3,MRPL54,NCLN,NDUFA11,NDUFB7,NDUFS7,PLEKHJ1, POLR2E,SGTA,SIRT6,SLC39A3,TIMM13,UQCR11,WDR18 | ATAD3A,UQCC3,DNPH1,DDX49,DGCR6L,MZT2B,HSPBP1, MLST8,MPG,MRPL4,MRPS12,MRPS26,MRPS34,NUBP2, PRPF31,RFXANK,RUVBL2,SSNA1,TIMM13,TMED1,TOMM40 |
ARMC6,ATP5D,UQCC3,C19orf24,C19orf70,CLPP,FBXW9, GADD45GIP1,LSM4,LSM7,MRPL12,MRPL4,NDUFA7,NDUFS7, PLEKHJ1,POLR2E,PRDX2,SGTA,THOP1,TIMM13,UQCR11 | ATP5G1,DCXR,FBXW9,ITPA,KRTCAP3,LSM4,MLST8, MRPL12,MRPL2,MRPL4,MRPS12,MRPS34,MTFP1,NDUFS6, SCO2,SF3B5,SLC25A39,THOC6,TIMM13,TSPO,YIF1B |
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 TIMM13 |
There's no related Drug. |
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Cross referenced IDs for TIMM13 |
* 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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