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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for P4HA2 |
Basic gene info. | Gene symbol | P4HA2 |
Gene name | prolyl 4-hydroxylase, alpha polypeptide II | |
Synonyms | - | |
Cytomap | UCSC genome browser: 5q31 | |
Genomic location | chr5 :131528303-131562935 | |
Type of gene | protein-coding | |
RefGenes | NM_001017973.1, NM_001017974.1,NM_001142598.1,NM_001142599.1,NM_004199.2, | |
Ensembl id | ENSG00000072682 | |
Description | 4-PH alpha 24-PH alpha-2C-P4Halpha(II)collagen prolyl 4-hydroxylase alpha(II)procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide IIprocollagen-proline,2-oxoglutarate-4-dioxygenase subunit alpha-2prolyl 4-hydr | |
Modification date | 20141207 | |
dbXrefs | MIM : 600608 | |
HGNC : HGNC | ||
Ensembl : ENSG00000072682 | ||
HPRD : 11862 | ||
Vega : OTTHUMG00000059647 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_P4HA2 | |
BioGPS: 8974 | ||
Gene Expression Atlas: ENSG00000072682 | ||
The Human Protein Atlas: ENSG00000072682 | ||
Pathway | NCI Pathway Interaction Database: P4HA2 | |
KEGG: P4HA2 | ||
REACTOME: P4HA2 | ||
ConsensusPathDB | ||
Pathway Commons: P4HA2 | ||
Metabolism | MetaCyc: P4HA2 | |
HUMANCyc: P4HA2 | ||
Regulation | Ensembl's Regulation: ENSG00000072682 | |
miRBase: chr5 :131,528,303-131,562,935 | ||
TargetScan: NM_001017973 | ||
cisRED: ENSG00000072682 | ||
Context | iHOP: P4HA2 | |
cancer metabolism search in PubMed: P4HA2 | ||
UCL Cancer Institute: P4HA2 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for P4HA2(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: P4HA2 |
Familial Cancer Database: P4HA2 |
* This gene is included in those cancer gene databases. |
Oncogene 1 | Significant driver gene in |
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/ |
Metabolic Pathway Description | |
KEGG_ARGININE_AND_PROLINE_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: P4HA2 |
MedGen: P4HA2 (Human Medical Genetics with Condition) | |
ClinVar: P4HA2 | |
Phenotype | MGI: P4HA2 (International Mouse Phenotyping Consortium) |
PhenomicDB: P4HA2 |
Mutations for P4HA2 |
* 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows P4HA2 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
Other DBs for Structural Variants |
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Copy 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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=35) | (# total SNVs=15) |
(# total SNVs=0) | (# total SNVs=0) |
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Top 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 position | Mutation(aa) | Unique sampleID count |
chr5:131534584-131534584 | p.F431F | 3 |
chr5:131534590-131534590 | p.P429P | 3 |
chr5:131539494-131539494 | p.R400C | 3 |
chr5:131530610-131530610 | p.? | 3 |
chr5:131534583-131534583 | p.D432N | 2 |
chr5:131543412-131543412 | p.A357T | 2 |
chr5:131543466-131543466 | p.V339I | 2 |
chr5:131544873-131544873 | p.R287R | 2 |
chr5:131543475-131543475 | p.P336S | 2 |
chr5:131546162-131546162 | p.S175L | 2 |
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SNV Counts per Each Loci in TCGA data |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 1 | 1 |   | 4 | 1 |   | 2 |   | 1 |   |   | 5 | 3 |   |   | 1 | 6 | 8 |   | 12 |
# mutation | 1 | 1 |   | 4 | 1 |   | 2 |   | 1 |   |   | 5 | 3 |   |   | 1 | 5 | 7 |   | 15 |
nonsynonymous SNV |   | 1 |   | 2 |   |   | 1 |   |   |   |   | 3 | 2 |   |   |   | 3 | 6 |   | 11 |
synonymous SNV | 1 |   |   | 2 | 1 |   | 1 |   | 1 |   |   | 2 | 1 |   |   | 1 | 2 | 1 |   | 4 |
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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Top 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 Position | Mutation(aa) | Unique sampleID count |
chr5:131539494 | p.R400C,P4HA2 | 2 |
chr5:131539797 | p.A377T,P4HA2 | 2 |
chr5:131543466 | p.V339I,P4HA2 | 2 |
chr5:131543487 | p.L33M,P4HA2 | 1 |
chr5:131530693 | p.F454L,P4HA2 | 1 |
chr5:131546185 | p.Y290Y,P4HA2 | 1 |
chr5:131534590 | p.F23F,P4HA2 | 1 |
chr5:131543569 | p.V451V,P4HA2 | 1 |
chr5:131530707 | p.R287R,P4HA2 | 1 |
chr5:131546193 | p.E22K,P4HA2 | 1 |
Other DBs for Point Mutations |
Copy Number for P4HA2 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 P4HA2 |
Gene 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. |
Differential 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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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-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 |
BGLAP,CCK,CDH15,CPN2,DMP1,GPC1,IBSP, IFITM5,LEPRE1,LOC284688,LRRTM4,MEPE,MRC2,P4HA2, PHOSPHO1,PRSS35,PTH1R,SLC36A2,SOST,SP7,TPST1 | B3GNT9,KIAA0930,CD276,CERCAM,CNPY4,DBN1,FAM109B, FAM43B,FKBP10,ISLR,LAMP1,LEPREL2,LOXL1,MRC2, P4HA2,PCDHGC3,PCOLCE,PPIC,RCN3,THBS3,TIMP1 | ||||
B4GALT1,TMEM263,CHPF,CSRNP3,CTNNA1,EGLN3,FAM114A1, FLJ23867,GJA8,GLG1,HPCAL1,OS9,P4HA1,P4HA2, PLOD1,SLC16A3,SLC22A4,TFF3,TMED9,TMEM184B,TNIP1 | AOC1,ARHGEF11,ATG9A,COBL,COL17A1,ARHGAP35,HECA, IL17RE,ITGA3,KIAA1211,OS9,P4HA2,PIGS,PLXNB2, PRKCSH,PXN,RAB11FIP1,SGK223,SPINT1,SRC,ZNF592 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for P4HA2 |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00139 | prolyl 4-hydroxylase, alpha polypeptide II | approved; nutraceutical | Succinic acid | ||
DB00172 | prolyl 4-hydroxylase, alpha polypeptide II | approved; nutraceutical | L-Proline |
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Cross referenced IDs for P4HA2 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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