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 COASY
Basic gene info.Gene symbolCOASY
Gene nameCoA synthase
SynonymsDPCK|NBIA6|NBP|PPAT|UKR1|pOV-2
CytomapUCSC genome browser: 17q12-q21
Genomic locationchr17 :40714091-40718295
Type of geneprotein-coding
RefGenesNM_001042529.2,
NM_001042532.3,NM_025233.6,NM_001042530.1,NM_001042531.1,
Ensembl idENSG00000068120
Descriptionbifunctional coenzyme A synthasebifunctional phosphopantetheine adenylyl transferase/dephospho CoA kinasenucleotide binding proteinphosphopantetheine adenylyltransferase / dephosphocoenzyme A kinase
Modification date20141207
dbXrefs MIM : 609855
HGNC : HGNC
Ensembl : ENSG00000068120
HPRD : 13080
Vega : OTTHUMG00000180245
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_COASY
BioGPS: 80347
Gene Expression Atlas: ENSG00000068120
The Human Protein Atlas: ENSG00000068120
PathwayNCI Pathway Interaction Database: COASY
KEGG: COASY
REACTOME: COASY
ConsensusPathDB
Pathway Commons: COASY
MetabolismMetaCyc: COASY
HUMANCyc: COASY
RegulationEnsembl's Regulation: ENSG00000068120
miRBase: chr17 :40,714,091-40,718,295
TargetScan: NM_001042529
cisRED: ENSG00000068120
ContextiHOP: COASY
cancer metabolism search in PubMed: COASY
UCL Cancer Institute: COASY
Assigned class in ccmGDBC

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

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

Mutations for COASY
* 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 COASY related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI650663COASY12126174071818740718301PPAN120378191022085910221276
BP275946COASY1437174071416940714997LOC100507412430499?109705109774
DC383781TAF1D164119346552793465590COASY65563174071416940714791
BG120370COASY161174071672140716794COASY52757174071681640718145
BE252620COASY1266174071657040717050DTD1264586201857674918725309
BQ212022COASY14115174071672140716835COASY106849174071681640718161
CR739363COASY1194174071418740714380PPAN189483191021878710220884

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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=35)
Stat. for Synonymous SNVs
(# total SNVs=11)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=1)

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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
chr17:40714723-40714723p.S28L3
chr17:40714959-40714959p.L107F2
chr17:40716901-40716901p.E408Q2
chr17:40714961-40714961p.L107L2
chr17:40716022-40716022p.V248V2
chr17:40714916-40714916p.T92T1
chr17:40716813-40716813p.L378L1
chr17:40715174-40715174p.S178S1
chr17:40717505-40717505p.V468V1
chr17:40714664-40714665p.(=)1

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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
# sample2325  2 31 732 132 10
# mutation2324  2 31 732 132 11
nonsynonymous SNV1213  1 2  612  21 10
synonymous SNV1111  1 11 12  111 1
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
chr17:40717718p.R429W,COASY2
chr17:40717048p.Y359C,COASY2
chr17:40716755p.A509A,COASY2
chr17:40714959p.L8L,COASY1
chr17:40717709p.S178S,COASY1
chr17:40716081p.L378L,COASY1
chr17:40714664p.R21G,COASY1
chr17:40716813p.G197D,COASY1
chr17:40714971p.A383A,COASY1
chr17:40716143p.A23V,COASY1

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 COASY 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 COASY

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

AARSD1,ACBD4,BECN1,CCDC103,COA3,CHCHD5,COASY,
FAM134C,G6PC3,GAMT,GHDC,HEXIM2,KAT2A,KRT19,
NAGLU,PLEKHH3,RAB5C,SLC25A39,STK16,TMUB2,VPS25
ARRDC1,ATP13A1,ATP13A2,HID1,C9orf114,CACFD1,COASY,
COMT,COQ4,DAK,DUS1L,FUK,GAK,GSS,
IGSF8,LLGL2,NARFL,NDOR1,PAK4,PICK1,SGSM3

AARSD1,CCDC137,CDC6,COASY,DBF4B,DUS1L,EFTUD2,
ERAL1,GIT1,GPS1,KAT2A,MLX,MRM1,PNPO,
POLDIP2,SLC25A19,SLC25A39,SMARCD2,TSEN54,TUBG1,VPS25
ABCF3,AP1M2,APEH,APEX2,ARHGEF16,CKMT1B,COASY,
E2F2,FBXL6,SLC52A2,IRAK1,LEMD2,PITPNM1,SH3BP1,
SLC25A10,SMARCD2,STXBP2,TALDO1,TLCD1,TTLL12,USP43
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 COASY
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00151CoA synthaseapproved; nutraceuticalL-Cysteine


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Cross referenced IDs for COASY
* 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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