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 P4HA3
Basic gene info.Gene symbolP4HA3
Gene nameprolyl 4-hydroxylase, alpha polypeptide III
Synonyms-
CytomapUCSC genome browser: 11q13.4
Genomic locationchr11 :73977701-74022699
Type of geneprotein-coding
RefGenesNM_001288748.1,
NM_182904.4,NR_110031.1,
Ensembl idENSG00000149380
Description4-PH alpha-3C-P4H alpha IIIcollagen prolyl 4-hydroxylase alpha(III)procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide IIIprolyl 4-hydroxylase subunit alpha-3
Modification date20141207
dbXrefs MIM : 608987
HGNC : HGNC
Ensembl : ENSG00000149380
HPRD : 16413
Vega : OTTHUMG00000165254
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_P4HA3
BioGPS: 283208
Gene Expression Atlas: ENSG00000149380
The Human Protein Atlas: ENSG00000149380
PathwayNCI Pathway Interaction Database: P4HA3
KEGG: P4HA3
REACTOME: P4HA3
ConsensusPathDB
Pathway Commons: P4HA3
MetabolismMetaCyc: P4HA3
HUMANCyc: P4HA3
RegulationEnsembl's Regulation: ENSG00000149380
miRBase: chr11 :73,977,701-74,022,699
TargetScan: NM_001288748
cisRED: ENSG00000149380
ContextiHOP: P4HA3
cancer metabolism search in PubMed: P4HA3
UCL Cancer Institute: P4HA3
Assigned class in ccmGDBC

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Phenotypic Information for P4HA3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: P4HA3
Familial Cancer Database: P4HA3
* 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_ARGININE_AND_PROLINE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: P4HA3
MedGen: P4HA3 (Human Medical Genetics with Condition)
ClinVar: P4HA3
PhenotypeMGI: P4HA3 (International Mouse Phenotyping Consortium)
PhenomicDB: P4HA3

Mutations for P4HA3
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows P4HA3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE702520ASAP1411118131164982131165052P4HA3104231117399818773998315

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 # sample3  2  4   1   1  
GAIN (# sample)3  1  1   1   1  
LOSS (# sample)   1  3          
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=36)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=1)
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
chr11:74000171-74000171p.G241E3
chr11:73988031-73988031p.T445M2
chr11:73978334-73978334p.Q532K2
chr11:73996902-73996902p.F354F2
chr11:73996950-73996950p.R338R2
chr11:73980719-73980719p.N482S2
chr11:73988187-73988187p.A393D2
chr11:74015355-74015355p.R101R2
chr11:73996970-73996970p.L332M1
chr11:74013510-74013510p.G157G1

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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
# sample 2 3  1 1  231 1135 5
# mutation 2 3  1 1  331 1145 5
nonsynonymous SNV 2 2  1 1  22  185 3
synonymous SNV   1       111  6  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
chr11:74015355p.G241E,P4HA32
chr11:74000171p.R101R,P4HA32
chr11:74013546p.D145E,P4HA31
chr11:73996902p.R251R,P4HA31
chr11:74009335p.G135E,P4HA31
chr11:74013577p.S248C,P4HA31
chr11:73997013p.R114R,P4HA31
chr11:74009355p.A587T1
chr11:74015318p.L230W,P4HA31
chr11:73978162p.P542T1

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 P4HA3 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 P4HA3

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

AEBP1,C1QTNF6,CMTM3,COL1A1,COL1A2,COL3A1,COL5A1,
COL5A2,COL6A3,COPZ2,EFEMP2,FAP,GLT8D2,HTRA1,
LOXL1,MMP2,P4HA3,PDGFRB,PDGFRL,SERPINF1,SRPX2
AQP9,ASPN,BASP1,BGN,CALHM2,CCDC109B,CCL7,
CLLU1OS,CPVL,CTHRC1,ELN,EVI2A,FAP,FGF16,
FGR,HEXB,IL10,MFAP2,P4HA3,RFPL4B,TMEM119

ANGPTL2,CERCAM,COL1A1,COL1A2,COL3A1,COL5A1,COL5A2,
COL6A2,COL6A3,DSEL,FBN1,FNDC1,FSTL1,GPC6,
IL1R1,KIAA1462,MRC2,P4HA3,PDGFRB,SPARC,THY1
ADAM23,ALDH1A2,ANXA5,DYX1C1,FAM92A1,FAP,GPR176,
GPX8,LNP1,MAPKAP1,OLFML2B,P4HA3,PALMD,SETD7,
SRPX2,STC2,THBS2,THY1,TIMP1,TSHZ2,WISP1
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 P4HA3


There's no related Drug.
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Cross referenced IDs for P4HA3
* 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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