Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 P4HA1
Basic gene info.Gene symbolP4HA1
Gene nameprolyl 4-hydroxylase, alpha polypeptide I
SynonymsP4HA
CytomapUCSC genome browser: 10q21.3-q23.1
Genomic locationchr10 :74766979-74856732
Type of geneprotein-coding
RefGenesNM_000917.3,
NM_001017962.2,NM_001142595.1,NM_001142596.1,
Ensembl idENSG00000122884
DescriptionC-P4Halpha(I)collagen prolyl 4-hydroxylase alpha(I)procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide Iprocollagen-proline,2-oxoglutarate-4-dioxygenase subunit alpha-1prolyl 4-hydroxylase subunit alpha-1
Modification date20141207
dbXrefs MIM : 176710
HGNC : HGNC
Ensembl : ENSG00000122884
HPRD : 08901
Vega : OTTHUMG00000018449
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_P4HA1
BioGPS: 5033
Gene Expression Atlas: ENSG00000122884
The Human Protein Atlas: ENSG00000122884
PathwayNCI Pathway Interaction Database: P4HA1
KEGG: P4HA1
REACTOME: P4HA1
ConsensusPathDB
Pathway Commons: P4HA1
MetabolismMetaCyc: P4HA1
HUMANCyc: P4HA1
RegulationEnsembl's Regulation: ENSG00000122884
miRBase: chr10 :74,766,979-74,856,732
TargetScan: NM_000917
cisRED: ENSG00000122884
ContextiHOP: P4HA1
cancer metabolism search in PubMed: P4HA1
UCL Cancer Institute: P4HA1
Assigned class in ccmGDBC

Top
Phenotypic Information for P4HA1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: P4HA1
Familial Cancer Database: P4HA1
* 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: P4HA1
MedGen: P4HA1 (Human Medical Genetics with Condition)
ClinVar: P4HA1
PhenotypeMGI: P4HA1 (International Mouse Phenotyping Consortium)
PhenomicDB: P4HA1

Mutations for P4HA1
* 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
* 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
ovaryP4HA1chr107481845474818474P4HA1chr107481855674818576
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 P4HA1 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

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample2  2             
GAIN (# sample)2  2             
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)

Top
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=4

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=24)
Stat. for Synonymous SNVs
(# total SNVs=9)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

Top
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
chr10:74813221-74813221p.G197G4
chr10:74833540-74833540p.S41F2
chr10:74806745-74806745p.R339C2
chr10:74828715-74828715p.R118*2
chr10:74790090-74790090p.R396Q2
chr10:74768012-74768012p.R525*2
chr10:74803649-74803649p.K382E2
chr10:74806829-74806829p.R311C2
chr10:74813167-74813167p.V215V2
chr10:74806852-74806852p.R303L1

Top
check002.gifSNV 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 ID1234567891011121314151617181920
# sample 1 7  1    53111104 6
# mutation 1 7  1    5311194 7
nonsynonymous SNV 1 2  1    33 1183 6
synonymous SNV   5       2 1  11 1
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])

Top
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
chr10:74813221p.G197G,P4HA13
chr10:74790090p.R396Q,P4HA12
chr10:74806745p.R339C,P4HA12
chr10:74810882p.A483V,P4HA11
chr10:74833540p.R311H,P4HA11
chr10:74770789p.R90H,P4HA11
chr10:74806754p.W467R,P4HA11
chr10:74810943p.R311C,P4HA11
chr10:74833576p.K72Q,P4HA11
chr10:74774018p.D441N,P4HA11

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 P4HA1 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]

Top
Gene Expression for P4HA1

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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
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

ADK,ANXA7,AP3M1,ASCC1,BNIP3,MICU1,MCU,
ECD,EGLN3,EIF4EBP2,ERO1L,FAM149B1,FUT11,LDHA,
MRPS16,P4HA1,PGK1,SAR1A,SEC24C,VCL,VDAC2
ABCC4,ADD3,CNTNAP2,ELOVL7,EXOC6,FAR2,G3BP2,
HERC3,HIST1H4H,HSD3B2,IDE,IDI1,MAPK6,NSF,
P4HA1,SAR1B,SCP2,SLC41A2,SMPDL3A,SPPL2A,SYT6

ALDOA,ALDOC,BNIP3L,C4orf3,CA9,EGLN3,ENO2,
ERO1L,FUT11,GBE1,HSP90B1,HSPA5,LDHA,NDRG1,
P4HA1,P4HB,PFKFB3,PGAM1,PKM,PLOD1,SLC16A3
MAB21L3,CDK19,EGLN3,FAM13A,GABRA2,LIPC,LRP4,
MUC20,NDRG1,NETO2,OPN3,P4HA1,PLOD2,RNASEL,
RNF170,SCARB1,SLC11A2,ST8SIA6,TCTN3,TSTD2,VWA5A
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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for P4HA1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00126prolyl 4-hydroxylase, alpha polypeptide Iapproved; nutraceuticalVitamin C
DB00139prolyl 4-hydroxylase, alpha polypeptide Iapproved; nutraceuticalSuccinic acid
DB00172prolyl 4-hydroxylase, alpha polypeptide Iapproved; nutraceuticalL-Proline
DB01275prolyl 4-hydroxylase, alpha polypeptide IapprovedHydralazine


Top
Cross referenced IDs for P4HA1
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas