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 HPD
Basic gene info.Gene symbolHPD
Gene name4-hydroxyphenylpyruvate dioxygenase
Synonyms4-HPPD|4HPPD|GLOD3|HPPDASE|PPD
CytomapUCSC genome browser: 12q24.31
Genomic locationchr12 :122277432-122326517
Type of geneprotein-coding
RefGenesNM_001171993.1,
NM_002150.2,
Ensembl idENSG00000158104
Description4-hydroxyphenylpyruvic acid oxidaseglyoxalase domain containing 3
Modification date20141207
dbXrefs MIM : 609695
HGNC : HGNC
Ensembl : ENSG00000158104
HPRD : 02041
Vega : OTTHUMG00000169081
ProteinUniProt: P32754
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HPD
BioGPS: 3242
Gene Expression Atlas: ENSG00000158104
The Human Protein Atlas: ENSG00000158104
PathwayNCI Pathway Interaction Database: HPD
KEGG: HPD
REACTOME: HPD
ConsensusPathDB
Pathway Commons: HPD
MetabolismMetaCyc: HPD
HUMANCyc: HPD
RegulationEnsembl's Regulation: ENSG00000158104
miRBase: chr12 :122,277,432-122,326,517
TargetScan: NM_001171993
cisRED: ENSG00000158104
ContextiHOP: HPD
cancer metabolism search in PubMed: HPD
UCL Cancer Institute: HPD
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for HPD(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_TYROSINE_METABOLISM
KEGG_PHENYLALANINE_METABOLISM
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

check002.gifOthers
OMIM 140350; phenotype.
276710; phenotype.
609695; gene.
Orphanet 2118; Hawkinsinuria.
69723; Tyrosinemia type 3.
DiseaseKEGG Disease: HPD
MedGen: HPD (Human Medical Genetics with Condition)
ClinVar: HPD
PhenotypeMGI: HPD (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
breastHPDchr12122319869122319869chr133716633237166332
ovaryHPDchr12122306411122306431WDR66chr12122391042122391062
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows HPD related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BP348274HPD138212122277581122296765HPD38158212122287652122294294
CD614163ADAM191585156907912156907969HPD5974012122285045122296745

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 # sample          1 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=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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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
chr12:122281717-122281718p.G285fs*306
chr12:122277840-122277840p.Q357*2
chr12:122294305-122294305p.G83G2
chr12:122292680-122292680p.A115T2
chr12:122292681-122292681p.G114G2
chr12:122277716-122277716p.L367R1
chr12:122292601-122292601p.?1
chr12:122281692-122281692p.S293F1
chr12:122294236-122294236p.I106I1
chr12:122284839-122284839p.E254K1

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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
# sample33 61 2 11 522  6211
# mutation33 61 2 11 622  7211
nonsynonymous SNV21 4  1 11 222  5211
synonymous SNV12 21 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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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
chr12:122294305p.G83G,HPD2
chr12:122281642p.A306T,HPD1
chr12:122295334p.T138A,HPD1
chr12:122285060p.A32V1
chr12:122292685p.S293F,HPD1
chr12:122281654p.G129W,HPD1
chr12:122295337p.W25L1
chr12:122286936p.P292L,HPD1
chr12:122292689p.A115T,HPD1
chr12:122281692p.T2T1

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 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

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

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
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 HPD
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryChEMBL CHEMBL1861; -.
Organism-specific databasesPharmGKB PA29420; -.
Organism-specific databasesCTD 3242; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB001434-hydroxyphenylpyruvate dioxygenaseapproved; nutraceuticalGlutathione
DB001204-hydroxyphenylpyruvate dioxygenaseapproved; nutraceuticalL-Phenylalanine
DB001354-hydroxyphenylpyruvate dioxygenaseapproved; nutraceuticalL-Tyrosine
DB003604-hydroxyphenylpyruvate dioxygenaseapproved; investigationalTetrahydrobiopterin


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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



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