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 PAH
Basic gene info.Gene symbolPAH
Gene namephenylalanine hydroxylase
SynonymsPH|PKU|PKU1
CytomapUCSC genome browser: 12q22-q24.2
Genomic locationchr12 :103232103-103311381
Type of geneprotein-coding
RefGenesNM_000277.1,
Ensembl idENSG00000171759
Descriptionphe-4-monooxygenasephenylalanine 4-monooxygenasephenylalanine-4-hydroxylase
Modification date20141219
dbXrefs MIM : 612349
HGNC : HGNC
Ensembl : ENSG00000171759
HPRD : 08943
Vega : OTTHUMG00000169966
ProteinUniProt: P00439
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PAH
BioGPS: 5053
Gene Expression Atlas: ENSG00000171759
The Human Protein Atlas: ENSG00000171759
PathwayNCI Pathway Interaction Database: PAH
KEGG: PAH
REACTOME: PAH
ConsensusPathDB
Pathway Commons: PAH
MetabolismMetaCyc: PAH
HUMANCyc: PAH
RegulationEnsembl's Regulation: ENSG00000171759
miRBase: chr12 :103,232,103-103,311,381
TargetScan: NM_000277
cisRED: ENSG00000171759
ContextiHOP: PAH
cancer metabolism search in PubMed: PAH
UCL Cancer Institute: PAH
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PAH in cancer cell metabolism1. Mantey JA, Rekhadevi PV, Diggs DL, Ramesh A (2014) Metabolism of benzo (a) pyrene by subcellular fractions of gastrointestinal (GI) tract and liver in Apc Min mouse model of colon cancer. Tumor Biology 35: 4929-4935. go to article

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Phenotypic Information for PAH(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PAH
Familial Cancer Database: PAH
* 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_PHENYLALANINE_METABOLISM
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

check002.gifOthers
OMIM 261600; phenotype.
612349; gene.
Orphanet 2209; Maternal hyperphenylalaninemia.
293284; Tetrahydrobiopterin-responsive hyperphenylalaninemia/phenylketonuria.
79253; Mild phenylketonuria.
79254; Classical phenylketonuria.
79651; Mild hyperphenylalaninemia.
DiseaseKEGG Disease: PAH
MedGen: PAH (Human Medical Genetics with Condition)
ClinVar: PAH
PhenotypeMGI: PAH (International Mouse Phenotyping Consortium)
PhenomicDB: PAH

Mutations for PAH
* 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
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasPAHchr12103278332103278352PAHchr12103278467103278487
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 PAH 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
There's no copy number variation information in COSMIC data for this gene.

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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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=63)
Stat. for Synonymous SNVs
(# total SNVs=19)
Stat. for Deletions
(# total SNVs=3)
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
chr12:103288633-103288633p.E78K3
chr12:103240729-103240729p.E305K3
chr12:103237469-103237469p.L385H3
chr12:103288533-103288533p.R111Q3
chr12:103249075-103249075p.E182G2
chr12:103249000-103249000p.N207S2
chr12:103246597-103246597p.E280K2
chr12:103234265-103234265p.F410I2
chr12:103240696-103240696p.E316K2
chr12:103246614-103246614p.K274T2

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample32 202 6 41 644  157 2
# mutation32 212 6 41 744  157 2
nonsynonymous SNV22 152 4 31 531  95 2
synonymous SNV1  6  2 1  213  62  
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
chr12:103249074p.R111Q3
chr12:103288533p.E182E3
chr12:103245469p.S303F2
chr12:103249075p.G10S2
chr12:103310881p.K274T2
chr12:103246614p.E182G2
chr12:103237469p.A447V1
chr12:103249038p.L347L1
chr12:103240685p.L249L1
chr12:103271254p.M180L1

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 PAH 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 PAH

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

AATK,ADARB2,ARSG,ASB16,BAIAP3,CCDC151,GDF15,
GOLGA2P3Y,PAH,PSG10P,PSG4,PSG5,PSG6,PSG9,
RTP2,SEMA3B,SLC16A6,TLX2,UNC5CL,VWA5B2,WNT3
AK5,C1orf74,C3orf14,CD9,DKFZP586I1420,ERP27,FAAH2,
HHAT,IRF6,KIF5C,LIPH,MYO6,PAH,PAK6,
PLEKHA6,POF1B,SDC4,SHISA2,VAV3,VEPH1,WISP3

ADAMTS20,ALDH4A1,AMACR,CDH26,CT47A1,ENGASE,EYA1,
MROH5,GCG,GRPR,ITGA2B,LOC340357,LOC541473,METAP1D,
PAH,PMFBP1,QPRT,SLC5A6,VIL1,XAGE2,ZNRF3
AMBP,APOA2,C3P1,C8B,CEL,CPB2,CYP2E1,
DNAJB8,F2,FGB,FGG,HAO1,KIR3DP1,KRTAP4-11,
KRTAP5-3,LECT2,LOC100129935,LINC00160,OR1N1,PAGE4,PAH,
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 PAH
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P00439; -.
ChemistryChEMBL CHEMBL3076; -.
ChemistryGuidetoPHARMACOLOGY 1240; -.
Organism-specific databasesPharmGKB PA32911; -.
Organism-specific databasesCTD 5053; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00120phenylalanine hydroxylaseapproved; nutraceuticalL-Phenylalanine
DB00360phenylalanine hydroxylaseapproved; investigationalTetrahydrobiopterin
DB00368phenylalanine hydroxylaseapprovedNorepinephrine
DB00668phenylalanine hydroxylaseapprovedEpinephrine
DB02562phenylalanine hydroxylaseexperimentalQuinonoid 7,8-Tetrahydrobiopterin
DB02692phenylalanine hydroxylaseexperimental(6r,1'r,2's)-5,6,7,8 Tetrahydrobiopterin
DB03673phenylalanine hydroxylaseexperimentalBeta(2-Thienyl)Alanine
DB04400phenylalanine hydroxylaseexperimental7,8-Dihydrobiopterin
DB04419phenylalanine hydroxylaseexperimentalNorleucine
DB06262phenylalanine hydroxylaseapproved; investigationalDroxidopa
DB03271phenylalanine hydroxylaseexperimental7,8-Dihydro-L-Biopterin
DB00143phenylalanine hydroxylaseapproved; nutraceuticalGlutathione
DB00135phenylalanine hydroxylaseapproved; nutraceuticalL-Tyrosine


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Cross referenced IDs for PAH
* 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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