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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for COX17 |
Basic gene info. | Gene symbol | COX17 |
Gene name | COX17 cytochrome c oxidase copper chaperone | |
Synonyms | - | |
Cytomap | UCSC genome browser: 3q13.33 | |
Genomic location | chr3 :119388371-119396243 | |
Type of gene | protein-coding | |
RefGenes | NM_005694.1, | |
Ensembl id | ENSG00000138495 | |
Description | COX17 cytochrome c oxidase assembly homologcytochrome c oxidase 17 copper chaperonecytochrome c oxidase assembly homolog 17cytochrome c oxidase copper chaperonehuman homolog of yeast mitochondrial copper recruitment | |
Modification date | 20141207 | |
dbXrefs | MIM : 604813 | |
HGNC : HGNC | ||
HPRD : 05314 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_COX17 | |
BioGPS: 10063 | ||
Gene Expression Atlas: ENSG00000138495 | ||
The Human Protein Atlas: ENSG00000138495 | ||
Pathway | NCI Pathway Interaction Database: COX17 | |
KEGG: COX17 | ||
REACTOME: COX17 | ||
ConsensusPathDB | ||
Pathway Commons: COX17 | ||
Metabolism | MetaCyc: COX17 | |
HUMANCyc: COX17 | ||
Regulation | Ensembl's Regulation: ENSG00000138495 | |
miRBase: chr3 :119,388,371-119,396,243 | ||
TargetScan: NM_005694 | ||
cisRED: ENSG00000138495 | ||
Context | iHOP: COX17 | |
cancer metabolism search in PubMed: COX17 | ||
UCL Cancer Institute: COX17 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for COX17(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: COX17 |
Familial Cancer Database: COX17 |
* 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/ |
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REACTOME_METABOLISM_OF_PROTEINS |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: COX17 |
MedGen: COX17 (Human Medical Genetics with Condition) | |
ClinVar: COX17 | |
Phenotype | MGI: COX17 (International Mouse Phenotyping Consortium) |
PhenomicDB: COX17 |
Mutations for COX17 |
* 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. |
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- Statistics for Tissue and Mutation type | Top |
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- 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'. |
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Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | COX17 | chr3 | 119394364 | 119394384 | ARHGAP31 | chr3 | 119126708 | 119126728 |
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) |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows COX17 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 |
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There's no copy number variation information in COSMIC data for this gene. |
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Stat. for Non-Synonymous SNVs (# total SNVs=3) | (# total SNVs=2) |
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(# total SNVs=0) | (# total SNVs=0) |
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* 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 |
chr3:119396135-119396135 | p.N8T | 1 |
chr3:119396138-119396138 | p.S7* | 1 |
chr3:119393997-119393997 | p.*64L | 1 |
chr3:119394035-119394035 | p.A51A | 1 |
chr3:119394073-119394073 | p.E39K | 1 |
chr3:119396062-119396062 | p.A32A | 1 |
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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 |   |   | 1 |   |   |   |   |   |   |   |   |   |   |   |   | 1 |
# mutation |   |   |   | 1 |   |   | 1 |   |   |   |   |   |   |   |   |   |   |   |   | 1 |
nonsynonymous SNV |   |   |   | 1 |   |   | 1 |   |   |   |   |   |   |   |   |   |   |   |   | 1 |
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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* 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 |
chr3:119394034 | p.H52N | 1 |
chr3:119394073 | p.E39K | 1 |
chr3:119396135 | p.N8T | 1 |
chr3:119396148 | p.L4V | 1 |
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* 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. |
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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 COX17 |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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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ATP5I,BLOC1S1,C16orf13,TMA7,CMC1,COX17,COX6A1, COX7C,HAGH,MRPL22,NDUFA1,NDUFA2,NDUFA7,NDUFB1, NDUFB4,NDUFC1,RNF7,TAF10,TBCA,PAM16,UBL5 | PRADC1,COX17,ENDOG,FUNDC2,LSM10,MRPS28,LINC00116, NDUFA1,NDUFA8,NDUFB10,NDUFB2,NDUFB3,NDUFB9,NDUFS3, NGRN,PINK1,SEPW1,SIRT2,TMEM11,UQCR10,UQCR11 |
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ATP5I,UQCC2,CCDC58,TMA7,CHCHD6,COX17,DNAJC19, HAGH,MRPL47,MRPS24,NDUFB4,NDUFS6,PFDN2,PFDN6, POLR2H,PTS,SEC61G,SHFM1,TBCA,TCEB2,USMG5 | ARPC2,ATOX1,ATP6V1E1,MCUR1,CHMP5,COX17,DYNLT1, FAM32A,LSM1,MRPS18C,NDUFC1,OAZ1,POLR2C,POMP, PSMA6,RHOC,RNF181,SF3B14,UBL5,VAMP8,YIPF5 |
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* 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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Pharmacological Information for COX17 |
There's no related Drug. |
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Cross referenced IDs for COX17 |
* 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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