Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for COX10
Basic gene info.Gene symbolCOX10
Gene nameCOX10 heme A:farnesyltransferase cytochrome c oxidase assembly factor
Synonyms-
CytomapUCSC genome browser: 17p12
Genomic locationchr17 :13972718-14111996
Type of geneprotein-coding
RefGenesNM_001303.3,
Ensembl idENSG00000006695
DescriptionCOX10 homolog, cytochrome c oxidase assembly protein, heme A: farnesyltransferasecytochrome c oxidase assembly homolog 10cytochrome c oxidase assembly proteincytochrome c oxidase subunit Xheme A: farnesyltransferaseheme O synthaseprotoheme IX farnes
Modification date20141207
dbXrefs MIM : 602125
HGNC : HGNC
Ensembl : ENSG00000006695
HPRD : 03673
Vega : OTTHUMG00000058814
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_COX10
BioGPS: 1352
Gene Expression Atlas: ENSG00000006695
The Human Protein Atlas: ENSG00000006695
PathwayNCI Pathway Interaction Database: COX10
KEGG: COX10
REACTOME: COX10
ConsensusPathDB
Pathway Commons: COX10
MetabolismMetaCyc: COX10
HUMANCyc: COX10
RegulationEnsembl's Regulation: ENSG00000006695
miRBase: chr17 :13,972,718-14,111,996
TargetScan: NM_001303
cisRED: ENSG00000006695
ContextiHOP: COX10
cancer metabolism search in PubMed: COX10
UCL Cancer Institute: COX10
Assigned class in ccmGDBC

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Phenotypic Information for COX10(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: COX10
Familial Cancer Database: COX10
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

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/

check002.gifMetabolic Pathway Description
KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: COX10
MedGen: COX10 (Human Medical Genetics with Condition)
ClinVar: COX10
PhenotypeMGI: COX10 (International Mouse Phenotyping Consortium)
PhenomicDB: COX10

Mutations for COX10
* 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows COX10 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DB233923COX101464171398220413982667PCGF34586004760119760261

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample2  1      1      
GAIN (# sample)1                
LOSS (# sample)1  1      1      
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=42)
Stat. for Synonymous SNVs
(# total SNVs=16)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=3)

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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr17:14110262-14110262p.R355H2
chr17:14110263-14110263p.R355R2
chr17:14110273-14110273p.R359C2
chr17:13980228-13980228p.L118F2
chr17:14110524-14110524p.P442P2
chr17:14095532-14095532p.D308N2
chr17:14095347-14095347p.P246L2
chr17:14005439-14005439p.L168L2
chr17:13972932-13972932p.S4P1
chr17:14005478-14005478p.P181P1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample21152 2  2154 1 65 5
# mutation21152 2  2154 1 65 5
nonsynonymous SNV21 52 1  1 42   42 3
synonymous SNV  1   1  1112 1 23 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr17:14095532p.D308N2
chr17:13980228p.L118F2
chr17:13977716p.R58H1
chr17:14110443p.S306R1
chr17:13980233p.X444X1
chr17:14110189p.E95E1
chr17:13977738p.S103L1
chr17:14110505p.G310S1
chr17:14005478p.P104S1
chr17:14110213p.W331R1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for COX10 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 COX10

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-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

: Open all plots for all cancer types

GID4,C1QBP,COPS3,COX10,DHX33,EIF4A1,EIF5AL1,
ELAC2,FAM64A,GEMIN4,GSG2,CLUH,MYBBP1A,NUP88,
RPA1,SCO1,SENP3,TSR1,TTC19,YWHAE,ZNF286A
ADSSL1,AGL,ASB8,CFL2,CKMT2,CLTCL1,COQ10A,
COX10,FAM166B,FXR1,GBAS,GYS1,NDUFS1,PAIP2B,
RPUSD4,SLC25A34,SPTB,TMEM143,TMEM52,TRIM55,USP13

ATPAF2,C1QBP,COPS3,COX10,EIF4A1,ELAC2,GEMIN4,
GLOD4,CLUH,MED9,MINK1,NUP88,RNMTL1,RPA1,
SCO1,SLC25A11,TSR1,TTC19,UBE2G1,WRAP53,YWHAE
ACTR5,FAM210A,C19orf57,COX10,DLAT,ERAL1,GOT1,
HN1L,MARS2,MCCC1,MEST,MLYCD,MRPS30,PDHA1,
PTCD3,QRSL1,RCL1,SHQ1,STARD7,SUPV3L1,TBRG4
check002.gifCo-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

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for COX10


There's no related Drug.
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Cross referenced IDs for COX10
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



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