Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 HMGCS2
Basic gene info.Gene symbolHMGCS2
Gene name3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)
Synonyms-
CytomapUCSC genome browser: 1p13-p12
Genomic locationchr1 :120290618-120311555
Type of geneprotein-coding
RefGenesNM_001166107.1,
NM_005518.3,
Ensembl idENSG00000134240
Description3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial)HMG-CoA synthasehydroxymethylglutaryl-CoA synthase, mitochondrial
Modification date20141207
dbXrefs MIM : 600234
HGNC : HGNC
Ensembl : ENSG00000134240
HPRD : 02580
Vega : OTTHUMG00000012101
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HMGCS2
BioGPS: 3158
Gene Expression Atlas: ENSG00000134240
The Human Protein Atlas: ENSG00000134240
PathwayNCI Pathway Interaction Database: HMGCS2
KEGG: HMGCS2
REACTOME: HMGCS2
ConsensusPathDB
Pathway Commons: HMGCS2
MetabolismMetaCyc: HMGCS2
HUMANCyc: HMGCS2
RegulationEnsembl's Regulation: ENSG00000134240
miRBase: chr1 :120,290,618-120,311,555
TargetScan: NM_001166107
cisRED: ENSG00000134240
ContextiHOP: HMGCS2
cancer metabolism search in PubMed: HMGCS2
UCL Cancer Institute: HMGCS2
Assigned class in ccmGDBC

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Phenotypic Information for HMGCS2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HMGCS2
Familial Cancer Database: HMGCS2
* 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_BUTANOATE_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: HMGCS2
MedGen: HMGCS2 (Human Medical Genetics with Condition)
ClinVar: HMGCS2
PhenotypeMGI: HMGCS2 (International Mouse Phenotyping Consortium)
PhenomicDB: HMGCS2

Mutations for HMGCS2
* 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 HMGCS2 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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1            1   
GAIN (# sample)1            1   
LOSS (# sample)                 
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=43)
Stat. for Synonymous SNVs
(# total SNVs=11)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr1:120301770-120301770p.R274L3
chr1:120295297-120295297p.G432D3
chr1:120298145-120298145p.F364F2
chr1:120298174-120298174p.A355S2
chr1:120302555-120302555p.R206H2
chr1:120307109-120307109p.G82E2
chr1:120301892-120301892p.T233T2
chr1:120295926-120295926p.R424Q2
chr1:120293530-120293530p.V474V2
chr1:120295927-120295927p.R424*2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample11 4  2 2  851 1235 9
# mutation11 4  2 2  951 1265 13
nonsynonymous SNV11 4  2 1  83  1153 9
synonymous SNV        1  121  112 4
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
chr1:120302555p.R206H2
chr1:120295926p.R382L,HMGCS22
chr1:120293530p.V432V,HMGCS22
chr1:120307109p.G82E,HMGCS22
chr1:120298174p.A313S,HMGCS22
chr1:120295184p.E60E,HMGCS21
chr1:120301892p.Q385Q,HMGCS21
chr1:120306903p.G297R,HMGCS21
chr1:120296009p.P201H1
chr1:120307181p.A58V,HMGCS21

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 HMGCS2 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 HMGCS2

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

ACSM1,C15orf43,CYP2J2,EIF3M,GJB1,HMGCS2,IDH1,
MS4A5,OR51A7,PSCA,PSMC5,RARA,REG4,SCP2,
SHROOM1,SMARCD2,SNORA70B,SPINK8,SULT1C3,TMIGD1,UGT2B28
ACSL3,ADAM2,AFMID,ALOX15B,B3GAT1,C15orf43,DHRS2,
DMRTC2,GGT1,GGTLC2,HMGCS2,HPGD,IDI1,MPV17L,
PNLIPRP3,SERHL2,SERHL,SPINK8,SRD5A1,UGT2B10,UGT2B11

AIFM3,ARHGDIG,C10orf99,CKB,ENTPD5,EPB41L4B,GGT6,
GPD1L,GPR39,HMGCS2,IHH,CCDC183,MAPRE3,MUC20,
OR7E91P,PBLD,PPARG,SGK2,SLC38A4,SUOX,TMEM63C
ACSF2,AGFG2,B4GALNT2,CPT2,DTX4,HMGCS2,LAMC3,
LOC100272146,ME3,MYO1D,NAALADL2,PAQR5,PWWP2A,SH3BGRL2,
SIRT5,SLC38A4,SUCLG2,TFRC,TRAF3IP2,UGT1A8,WDR78
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 HMGCS2


There's no related Drug.
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Cross referenced IDs for HMGCS2
* 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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