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 HPD

Basic gene info.	Gene symbol	HPD
	Gene name	4-hydroxyphenylpyruvate dioxygenase
	Synonyms	4-HPPD\|4HPPD\|GLOD3\|HPPDASE\|PPD
	Cytomap	UCSC genome browser: 12q24.31
	Genomic location	chr12 :122277432-122326517
	Type of gene	protein-coding
	RefGenes	NM_001171993.1, NM_002150.2,
	Ensembl id	ENSG00000158104
	Description	4-hydroxyphenylpyruvic acid oxidaseglyoxalase domain containing 3
	Modification date	20141207
dbXrefs	MIM : 609695
	HGNC : HGNC
	Ensembl : ENSG00000158104
	HPRD : 02041
	Vega : OTTHUMG00000169081
Protein	UniProt: P32754 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_HPD
	BioGPS: 3242
	Gene Expression Atlas: ENSG00000158104
	The Human Protein Atlas: ENSG00000158104
Pathway	NCI Pathway Interaction Database: HPD
	KEGG: HPD
	REACTOME: HPD
	ConsensusPathDB
	Pathway Commons: HPD
Metabolism	MetaCyc: HPD
	HUMANCyc: HPD
Regulation	Ensembl's Regulation: ENSG00000158104
	miRBase: chr12 :122,277,432-122,326,517
	TargetScan: NM_001171993
	cisRED: ENSG00000158104
Context	iHOP: HPD
	cancer metabolism search in PubMed: HPD
	UCL Cancer Institute: HPD
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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

Cancer Description
Cancer	CGAP: HPD
	Familial Cancer Database: HPD

* 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 UCEC ⁶,	Therapeutic Vulnerabilities in Cancer⁷

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,
6 http://www.nature.com/nature/journal/v497/n7447/full/nature12113.html,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
KEGG_TYROSINE_METABOLISM KEGG_PHENYLALANINE_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

Others
OMIM	140350; phenotype. 276710; phenotype. 609695; gene.
Orphanet	2118; Hawkinsinuria. 69723; Tyrosinemia type 3.
Disease	KEGG Disease: HPD
	MedGen: HPD (Human Medical Genetics with Condition)
	ClinVar: HPD
Phenotype	MGI: HPD (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: HPD

Mutations for HPD

* 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

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- 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
breast	HPD	chr12	122319869	122319869		chr13	37166332	37166332
ovary	HPD	chr12	122306411	122306431	WDR66	chr12	122391042	122391062

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 HPD 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
BP348274	HPD	1	382	12	122277581	122296765	HPD	381	582	12	122287652	122294294
CD614163	ADAM19	1	58	5	156907912	156907969	HPD	59	740	12	122285045	122296745

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

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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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=30)	Stat. for Synonymous SNVs (# total SNVs=13)

Stat. for Deletions (# total SNVs=6)	Stat. for Insertions (# total SNVs=0)
	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
chr12:122281717-122281718	p.G285fs*30	6
chr12:122277840-122277840	p.Q357*	2
chr12:122294305-122294305	p.G83G	2
chr12:122292680-122292680	p.A115T	2
chr12:122292681-122292681	p.G114G	2
chr12:122287671-122287671	p.V147G	1
chr12:122277654-122277654	p.G388R	1
chr12:122281677-122281677	p.Q298P	1
chr12:122292689-122292689	p.E112K	1
chr12:122284819-122284819	p.G260G	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=2

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	3	3		6	1		2		1	1		5	2	2			6	2	1	1
# mutation	3	3		6	1		2		1	1		6	2	2			7	2	1	1
nonsynonymous SNV	2	1		4			1		1	1		2	2	2			5	2	1	1
synonymous SNV	1	2		2	1		1					4					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
chr12:122294305	p.G83G,HPD	2
chr12:122295271	p.G261G,HPD	1
chr12:122277716	p.R111Q,HPD	1
chr12:122284839	p.E254K,HPD	1
chr12:122292681	p.Q108K,HPD	1
chr12:122295276	p.A244A,HPD	1
chr12:122277893	p.I106I,HPD	1
chr12:122284985	p.T219T,HPD	1
chr12:122292683	p.G92R,HPD	1
chr12:122295334	p.P189T,HPD	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 HPD 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 HPD

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


AFMID,AKR1C2,AKR1D1,C15orf43,CLPSL1,C6orf223,ARMC12, CCBL1,CDC42EP5,GGT1,GGTLC1,GGTLC2,HPD,KCNG2, LOC100129066,LOC285847,LOC644165,LOH12CR1,SERHL2,SERHL,SLED1	AADAT,APOD,CTNNA2,DHRS2,F9,GGTLC2,GSTM5, GUSB,HAAO,HIST1H2AE,HIST1H2BG,HPD,HSD3B2,LST-3TM12, NAT2,OR4D10,PPEF1,SERHL,SPINK8,SULT1C3,UGT2B10

ANGPTL1,ATP1A2,CASQ2,FBXL22,FXYD1,HPD,HSPB6, HSPB8,KCNMB1,LMOD1,MAMDC2,MORN5,MYL9,NECAB1, PDZRN4,PHKG1,PLN,POPDC2,SCRG1,SDPR,TACR2	AFM,C3P1,CYP2E1,DNAJB8,FGA,FGB,FGG, HPD,KIR3DP1,KRTAP4-11,KRTAP5-3,LECT2,LOC100129935,MBL2, LINC00160,OR1N1,PAGE4,SERPINC1

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 HPD

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	ChEMBL	CHEMBL1861; -.
Organism-specific databases	PharmGKB	PA29420; -.
Organism-specific databases	CTD	3242; -.

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
DB00143	4-hydroxyphenylpyruvate dioxygenase	approved; nutraceutical	Glutathione
DB00120	4-hydroxyphenylpyruvate dioxygenase	approved; nutraceutical	L-Phenylalanine
DB00135	4-hydroxyphenylpyruvate dioxygenase	approved; nutraceutical	L-Tyrosine
DB00360	4-hydroxyphenylpyruvate dioxygenase	approved; investigational	Tetrahydrobiopterin

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Cross referenced IDs for HPD

* 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