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 COQ2
Basic gene info.Gene symbolCOQ2
Gene namecoenzyme Q2 4-hydroxybenzoate polyprenyltransferase
SynonymsCL640|COQ10D1|MSA1
CytomapUCSC genome browser: 4q21.23
Genomic locationchr4 :84184976-84206067
Type of geneprotein-coding
RefGenesNM_015697.7,
Ensembl idENSG00000173085
Description4-hydroxybenzoate polyprenyltransferase, mitochondrialPHB:polyprenyltransferasecoenzyme Q2 homolog, prenyltransferasepara-hydroxybenzoate-polyprenyltransferase, mitochondrial
Modification date20141207
dbXrefs MIM : 609825
HGNC : HGNC
Ensembl : ENSG00000173085
HPRD : 13062
Vega : OTTHUMG00000160940
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_COQ2
BioGPS: 27235
Gene Expression Atlas: ENSG00000173085
The Human Protein Atlas: ENSG00000173085
PathwayNCI Pathway Interaction Database: COQ2
KEGG: COQ2
REACTOME: COQ2
ConsensusPathDB
Pathway Commons: COQ2
MetabolismMetaCyc: COQ2
HUMANCyc: COQ2
RegulationEnsembl's Regulation: ENSG00000173085
miRBase: chr4 :84,184,976-84,206,067
TargetScan: NM_015697
cisRED: ENSG00000173085
ContextiHOP: COQ2
cancer metabolism search in PubMed: COQ2
UCL Cancer Institute: COQ2
Assigned class in ccmGDBC

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Phenotypic Information for COQ2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: COQ2
Familial Cancer Database: COQ2
* 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
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: COQ2
MedGen: COQ2 (Human Medical Genetics with Condition)
ClinVar: COQ2
PhenotypeMGI: COQ2 (International Mouse Phenotyping Consortium)
PhenomicDB: COQ2

Mutations for COQ2
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows COQ2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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
There's no copy number variation information in COSMIC data for this gene.

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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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=18)
Stat. for Synonymous SNVs
(# total SNVs=4)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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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
chr4:84188773-84188773p.A356V1
chr4:84194714-84194714p.S209S1
chr4:84205996-84205996p.G24G1
chr4:84188847-84188847p.G331G1
chr4:84194739-84194739p.A201V1
chr4:84205998-84205998p.G24R1
chr4:84188912-84188912p.V310I1
chr4:84194754-84194754p.N196S1
chr4:84206028-84206028p.A14T1
chr4:84191125-84191125p.A267V1

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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
# sample   5       1 1  22 3
# mutation   5       1 1  22 3
nonsynonymous SNV   5       1    12 1
synonymous SNV             1  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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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
chr4:84188773p.M248I1
chr4:84188847p.N228H1
chr4:84193274p.R173H1
chr4:84194659p.R173S1
chr4:84200153p.L162F1
chr4:84185391p.P45L1
chr4:84200154p.D409D1
chr4:84185424p.V398V1
chr4:84200187p.V393I1
chr4:84185441p.N381D1

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 COQ2 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 COQ2

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

KNSTRN,CMC2,CCNA2,CCNB2,CDC20,CDCA8,CENPA,
CENPE,CENPN,CKS2,COQ2,H2AFZ,MAD2L1,MND1,
MRPS18C,NCAPG,OIP5,PTTG1,RAD51,SKA1,TUBA1C
AIMP2,AKR1B1,BIN1,C1orf127,CISD1,COQ2,COQ9,
COX5A,FKBP3,GOT1,MYL12A,NDUFA9,NDUFB3,PAQR9,
SLC16A10,TMEM233,TPI1,TPM3,UTP11L,VDAC1,VDAC3

CCNA2,CENPM,CHAC2,COQ2,DEPDC1,GLRX5,GNPNAT1,
GRSF1,H2AFZ,CENPU,MND1,MRPL1,MRPL16,NUDT6,
NUDT8,PCCB,PNP,POC1A,PPA2,RCC1,VRK1
PARPBP,CCT5,CENPN,CHEK2,COQ2,DBF4,GGCT,
GINS1,GINS2,HNRNPF,HPRT1,KIAA0101,MIPEP,NDUFA9,
PLEK2,POC1A,POLE2,RPN1,RTN4IP1,ALYREF,VRK1
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 COQ2


There's no related Drug.
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Cross referenced IDs for COQ2
* 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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