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 HDAC3

Basic gene info.	Gene symbol	HDAC3
	Gene name	histone deacetylase 3
	Synonyms	HD3\|RPD3\|RPD3-2
	Cytomap	UCSC genome browser: 5q31
	Genomic location	chr5 :141000442-141016423
	Type of gene	protein-coding
	RefGenes	NM_003883.3,
	Ensembl id	ENSG00000171720
	Description	SMAP45
	Modification date	20141222
dbXrefs	MIM : 605166
	HGNC : HGNC
	Ensembl : ENSG00000171720
	HPRD : 08950
	Vega : OTTHUMG00000129629
Protein	UniProt: O15379 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_HDAC3
	BioGPS: 8841
	Gene Expression Atlas: ENSG00000171720
	The Human Protein Atlas: ENSG00000171720
Pathway	NCI Pathway Interaction Database: HDAC3
	KEGG: HDAC3
	REACTOME: HDAC3
	ConsensusPathDB
	Pathway Commons: HDAC3
Metabolism	MetaCyc: HDAC3
	HUMANCyc: HDAC3
Regulation	Ensembl's Regulation: ENSG00000171720
	miRBase: chr5 :141,000,442-141,016,423
	TargetScan: NM_003883
	cisRED: ENSG00000171720
Context	iHOP: HDAC3
	cancer metabolism search in PubMed: HDAC3
	UCL Cancer Institute: HDAC3
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for HDAC3(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: HDAC3
	Familial Cancer Database: HDAC3

* 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
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM	605166; gene.
Orphanet
Disease	KEGG Disease: HDAC3
	MedGen: HDAC3 (Human Medical Genetics with Condition)
	ClinVar: HDAC3
Phenotype	MGI: HDAC3 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: HDAC3

Mutations for HDAC3

* 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

- Statistics for Tissue and Mutation type

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- For Inter-chromosomal Variations

There's no inter-chromosomal structural variation.

- For Intra-chromosomal Variations

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	HDAC3	chr5	141011717	141011917		chr5	141579479	141579679

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows HDAC3 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
BF871741	HDAC3	1	265	5	141004808	141005639	NSL1	250	270	1	212923249	212923269
AI133081	MALAT1	1	308	11	65268585	65268892	HDAC3	308	600	5	141005791	141008217
AF130111	MALAT1	1	308	11	65268585	65268892	HDAC3	308	1585	5	141000448	141008217
AV717686	HDAC3	1	307	5	141000772	141004802	S100B	295	690	21	48019141	48022311

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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=24)	Stat. for Synonymous SNVs (# total SNVs=10)

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
chr5:141009659-141009659	p.S105S	3
chr5:141005334-141005334	p.?	3
chr5:141014386-141014386	p.G91G	2
chr5:141009646-141009646	p.A110T	2
chr5:141004894-141004894	p.L366L	2
chr5:141005843-141005843	p.V280I	2
chr5:141007470-141007470	p.R274*	2
chr5:141007497-141007497	p.R265*	2
chr5:141008874-141008874	p.?	2
chr5:141009241-141009241	p.?	2

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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=3

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	1	1		3			1				1	1		1			7	8		10
# mutation	1	1		3			1				1	1		1			7	8		12
nonsynonymous SNV		1		3			1				1	1		1			5	6		9
synonymous SNV	1																2	2		3

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
chr5:141009679	p.G99W	3
chr5:141009646	p.A110T	2
chr5:141004824	p.E330K	1
chr5:141014504	p.F101S	1
chr5:141007696	p.R305R	1
chr5:141009658	p.V280I	1
chr5:141004855	p.P98S	1
chr5:141016121	p.S272I	1
chr5:141008152	p.G91G	1
chr5:141009672	p.T250T	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 HDAC3 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 HDAC3

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


ATOX1,B4GALT7,DDX41,HARS2,HARS,HDAC3,LMAN2, MBD3,MGAT1,NDUFS4,NDUFS6,RAB24,RBM22,RPS14, SLC35A4,SRA1,TMED9,TNIP1,TSPAN17,TWF2,ZMAT2	APH1A,CUTA,DGUOK,DIABLO,DYRK4,ERGIC3,FBL, GNB2L1,HDAC3,LCMT1,POLR2H,PPIH,PRCC,RFC2, RPL10,RPL10A,RPL13A,RPS4X,SNRPD2,SNRPF,SSR2

BTF3,CDC23,CDC25C,CDKN2AIPNL,ETF1,H2AFY,HARS, HDAC3,HINT1,HSPA9,MRPL22,NDUFA2,NHP2,PPP2CA, PTTG1,RBM22,SKP1,TBCA,TTC1,UBE2D2,UIMC1	ABT1,C18orf21,ZFAS1,C7orf55,DPY30,HDAC3,MRPL43, PMPCB,NELFE,RPL27A,RPL41,RPS10,RPS11,RPS14, RPS18,RPS21,RPS8,SNRPD2,SUMO3,TATDN3,WDR70

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 HDAC3

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	O15379; -.
Chemistry	ChEMBL	CHEMBL3038484; -.
Chemistry	GuidetoPHARMACOLOGY	2617; -.
Organism-specific databases	PharmGKB	PA29228; -.
Organism-specific databases	CTD	8841; -.

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
DB02546	histone deacetylase 3	approved; investigational	Vorinostat
DB00313	histone deacetylase 3	approved; investigational	Valproic Acid

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Cross referenced IDs for HDAC3

* 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