Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 HMGCS1

Basic gene info.	Gene symbol	HMGCS1
	Gene name	3-hydroxy-3-methylglutaryl-CoA synthase 1 (soluble)
	Synonyms	HMGCS
	Cytomap	UCSC genome browser: 5p14-p13
	Genomic location	chr5 :43289492-43313595
	Type of gene	protein-coding
	RefGenes	NM_001098272.2, NM_002130.7,
	Ensembl id	ENSG00000112972
	Description	3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) synthase3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble)hydroxymethylglutaryl-CoA synthase, cytoplasmic
	Modification date	20141207
dbXrefs	MIM : 142940
	HGNC : HGNC
	Ensembl : ENSG00000112972
	HPRD : 07515
	Vega : OTTHUMG00000162231
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_HMGCS1
	BioGPS: 3157
	Gene Expression Atlas: ENSG00000112972
	The Human Protein Atlas: ENSG00000112972
Pathway	NCI Pathway Interaction Database: HMGCS1
	KEGG: HMGCS1
	REACTOME: HMGCS1
	ConsensusPathDB
	Pathway Commons: HMGCS1
Metabolism	MetaCyc: HMGCS1
	HUMANCyc: HMGCS1
Regulation	Ensembl's Regulation: ENSG00000112972
	miRBase: chr5 :43,289,492-43,313,595
	TargetScan: NM_001098272
	cisRED: ENSG00000112972
Context	iHOP: HMGCS1
	cancer metabolism search in PubMed: HMGCS1
	UCL Cancer Institute: HMGCS1
Assigned class in ccmGDB	C

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Phenotypic Information for HMGCS1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: HMGCS1
	Familial Cancer Database: HMGCS1

* 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/

Metabolic Pathway Description
KEGG_BUTANOATE_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: HMGCS1
	MedGen: HMGCS1 (Human Medical Genetics with Condition)
	ClinVar: HMGCS1
Phenotype	MGI: HMGCS1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: HMGCS1

Mutations for HMGCS1

* 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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

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

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows HMGCS1 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
AK025736	ZC3HC1	1	259	7	129671759	129673797	HMGCS1	259	2646	5	43289498	43294957
BF476718	ABCA8	1	164	17	66863430	66863593	HMGCS1	165	525	5	43308876	43309236
AL048839	HMGCS1	23	133	5	43290973	43291083	HMGCS1	126	547	5	43290590	43291011
BG290679	HMGCS1	25	87	5	43290113	43290175	HMGCS1	81	683	5	43289500	43290105

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy 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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SNV 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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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=31)	Stat. for Synonymous SNVs (# total SNVs=8)

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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Top 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 position	Mutation(aa)	Unique sampleID count
chr5:43298129-43298129	p.P186S	3
chr5:43298903-43298903	p.K55N	2
chr5:43298710-43298710	p.I120V	2
chr5:43294891-43294891	p.L326L	2
chr5:43292647-43292647	p.R468W	1
chr5:43298855-43298855	p.T71T	1
chr5:43294964-43294964	p.?	1
chr5:43299062-43299062	p.P2P	1
chr5:43298164-43298164	p.V174A	1
chr5:43292694-43292694	p.T452M	1

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SNV Counts per Each Loci in TCGA data

: non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=1

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	2	4	1	2			2		1			6	2				2	1		6
# mutation	2	4	1	2			2		1			7	2				2	1		8
nonsynonymous SNV	1	2	1	1			2		1			6	1				2	1		6
synonymous SNV	1	2		1								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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr5:43298869	p.S67T,HMGCS1	2
chr5:43298903	p.K55K,HMGCS1	2
chr5:43298724	p.P496H,HMGCS1	1
chr5:43291309	p.C268S,HMGCS1	1
chr5:43295898	p.T452M,HMGCS1	1
chr5:43298779	p.Q243Q,HMGCS1	1
chr5:43292694	p.A424T,HMGCS1	1
chr5:43295906	p.K239N,HMGCS1	1
chr5:43298817	p.F423F,HMGCS1	1
chr5:43292989	p.A228A,HMGCS1	1

Other 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

Copy Number for HMGCS1 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 HMGCS1

Gene 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.

Differential 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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CNV 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

Co-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


ACAT2,C5orf22,C5orf34,DNAJC21,FDPS,GOLPH3,HMGCR, HMGCS1,IDI1,LDLR,NUP155,OPA1,PAIP1,PRKAA1, RAD1,DROSHA,MSMO1,SQLE,SREBF2,TARS,ZNF131	ABCC2,ADAM2,AWAT2,B3GAT1,C6orf223,CPB2,GSTT2, HMGCR,HMGCS1,LONP2,MPV17L,PNLIPRP3,MSMO1,SERHL2, SLC15A1,SLC5A11,SLCO1B1,SRD5A1,SV2C,TARP,UGT2B28

ACAT2,ALDOC,CYP1A1,CYP51A1,DHCR24,DHCR7,ELOVL6, FGFBP1,GAN,HMGCR,HMGCS1,IDI1,INSIG1,LSS, MVD,PANK3,PCSK9,MSMO1,SC5D,SCD,STARD4	C14orf1,C6orf223,CDY2B,CSRP3,CYP51A1,DHCR7,FDFT1, FGFBP1,HMGCS1,IDI1,INSIG1,LOC151658,MVD,MVK, NSDHL,OPN5,OR2F1,RXFP2,MSMO1,SC5D,SQLE

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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 HMGCS1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00363	3-hydroxy-3-methylglutaryl-CoA synthase 1 (soluble)	approved	Clozapine
DB00502	3-hydroxy-3-methylglutaryl-CoA synthase 1 (soluble)	approved	Haloperidol

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Cross referenced IDs for HMGCS1

* 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