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 P4HB
Basic gene info.Gene symbolP4HB
Gene nameprolyl 4-hydroxylase, beta polypeptide
SynonymsDSI|ERBA2L|GIT|P4Hbeta|PDI|PDIA1|PHDB|PO4DB|PO4HB|PROHB
CytomapUCSC genome browser: 17q25
Genomic locationchr17 :79801033-79818544
Type of geneprotein-coding
RefGenesNM_000918.3,
Ensembl idENSG00000185624
Descriptioncellular thyroid hormone-binding proteincollagen prolyl 4-hydroxylase betaglutathione-insulin transhydrogenasep55procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptideprolyl 4-hydroxylase subunit betaprotein disu
Modification date20141207
dbXrefs MIM : 176790
HGNC : HGNC
Ensembl : ENSG00000185624
HPRD : 07181
Vega : OTTHUMG00000150269
ProteinUniProt: P07237
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_P4HB
BioGPS: 5034
Gene Expression Atlas: ENSG00000185624
The Human Protein Atlas: ENSG00000185624
PathwayNCI Pathway Interaction Database: P4HB
KEGG: P4HB
REACTOME: P4HB
ConsensusPathDB
Pathway Commons: P4HB
MetabolismMetaCyc: P4HB
HUMANCyc: P4HB
RegulationEnsembl's Regulation: ENSG00000185624
miRBase: chr17 :79,801,033-79,818,544
TargetScan: NM_000918
cisRED: ENSG00000185624
ContextiHOP: P4HB
cancer metabolism search in PubMed: P4HB
UCL Cancer Institute: P4HB
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for P4HB(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: P4HB
Familial Cancer Database: P4HB
* 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
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS
REACTOME_LIPOPROTEIN_METABOLISM

check002.gifOthers
OMIM 176790; gene.
Orphanet
DiseaseKEGG Disease: P4HB
MedGen: P4HB (Human Medical Genetics with Condition)
ClinVar: P4HB
PhenotypeMGI: P4HB (International Mouse Phenotyping Consortium)
PhenomicDB: P4HB

Mutations for P4HB
* 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
ovaryP4HBchr177980709779807117chr177979881879798838
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 P4HB related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW410007RPS92465195470474254705054P4HB66545177980307479804852
DC413827P4HB2295177981720579818437PLEKHB22915192131905344131905573
BE878135HELZ1228176506944465069671P4HB221335177980103779801151
CN345438P4HB9411177981705779818398MAP4K44106222102459069102460700
BP290873P4HB1209177980140879801616UBE2E32093612181846811181846963

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             
LOSS (# sample)             1   
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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=29)
Stat. for Synonymous SNVs
(# total SNVs=22)
Stat. for Deletions
(# total SNVs=2)
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
chr17:79818260-79818260p.R30R6
chr17:79803083-79803083p.R461R3
chr17:79813041-79813041p.D201H2
chr17:79803437-79803437p.T453T2
chr17:79803764-79803764p.N387fs*1182
chr17:79817119-79817119p.R97H2
chr17:79804462-79804462p.R300H2
chr17:79803535-79803535p.V421I1
chr17:79813038-79813038p.G202W1
chr17:79804386-79804386p.T325T1

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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
# sample61 31 2    64   4617
# mutation71 31 2    65   4717
nonsynonymous SNV41 31 1    44   34 5
synonymous SNV3     1    21   1312
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
chr17:79804359p.D199H2
chr17:79813047p.L334L2
chr17:79804356p.L443L1
chr17:79805189p.T241T1
chr17:79803084p.A434V1
chr17:79817199p.V220A1
chr17:79801895p.E507G1
chr17:79813036p.E431Q1
chr17:79803437p.G202G1
chr17:79804386p.D506Y1

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 P4HB 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 P4HB

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

ANAPC11,ARHGDIA,OGFOD3,C17orf89,PRADC1,CALR,CCDC137,
DUS1L,GAA,GPS1,MRPL12,P4HB,PCYT2,PPIB,
PYCR1,SEC61A1,SLC25A10,SLC38A10,STRA13,ALYREF,TMEM104
C19orf10,CALR,CDK5,CNP,COMT,COPG1,CORO1B,
CYB561D2,DPP3,DUS1L,FDPS,GMPPB,SLC52A2,GSS,
HM13,LMAN2,MFSD7,NANS,P4HB,RRBP1,SLC39A7

AGR2,OGFOD3,C19orf10,CALR,CRELD2,ERO1L,GMPPA,
HSP90B1,HSPA5,LGALS3BP,MANF,NUCB2,P4HB,PDIA3,
PDIA3P1,PDIA4,PKM,PPIB,SEC61A1,SLC16A3,SRP68
ACOT7,ARPC1B,RTCB,CDCA3,CNDP2,CRCT1,DAP,
ENTPD7,GMPPA,GRAMD2,P4HB,SEC13,SEC24A,SLC31A1,
SLC35B1,SURF4,TFG,TSPO2,UNC5CL,WDR34,XPNPEP1
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 P4HB
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P07237; -.
ChemistryChEMBL CHEMBL2364681; -.
Organism-specific databasesPharmGKB PA32876; -.
Organism-specific databasesCTD 5034; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB03615prolyl 4-hydroxylase, beta polypeptideexperimentalRibostamycin
DB00171prolyl 4-hydroxylase, beta polypeptideapproved; nutraceuticalAdenosine triphosphate
DB00119prolyl 4-hydroxylase, beta polypeptideapproved; nutraceuticalPyruvic acid


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Cross referenced IDs for P4HB
* 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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