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 PRDX6
Basic gene info.Gene symbolPRDX6
Gene nameperoxiredoxin 6
Synonyms1-Cys|AOP2|HEL-S-128m|NSGPx|PRX|aiPLA2|p29
CytomapUCSC genome browser: 1q25.1
Genomic locationchr1 :173446485-173457946
Type of geneprotein-coding
RefGenesNM_004905.2,
Ensembl idENSG00000117592
Description1-Cys PRX1-Cys peroxiredoxin24 kDa proteinacidic calcium-independent phospholipase A2antioxidant protein 2epididymis secretory sperm binding protein Li 128mliver 2D page spot 40non-selenium glutathione peroxidaseperoxiredoxin-6red blood cells pag
Modification date20141207
dbXrefs MIM : 602316
HGNC : HGNC
Ensembl : ENSG00000117592
HPRD : 03817
Vega : OTTHUMG00000034804
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PRDX6
BioGPS: 9588
Gene Expression Atlas: ENSG00000117592
The Human Protein Atlas: ENSG00000117592
PathwayNCI Pathway Interaction Database: PRDX6
KEGG: PRDX6
REACTOME: PRDX6
ConsensusPathDB
Pathway Commons: PRDX6
MetabolismMetaCyc: PRDX6
HUMANCyc: PRDX6
RegulationEnsembl's Regulation: ENSG00000117592
miRBase: chr1 :173,446,485-173,457,946
TargetScan: NM_004905
cisRED: ENSG00000117592
ContextiHOP: PRDX6
cancer metabolism search in PubMed: PRDX6
UCL Cancer Institute: PRDX6
Assigned class in ccmGDBC

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Phenotypic Information for PRDX6(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PRDX6
Familial Cancer Database: PRDX6
* 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

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PRDX6
MedGen: PRDX6 (Human Medical Genetics with Condition)
ClinVar: PRDX6
PhenotypeMGI: PRDX6 (International Mouse Phenotyping Consortium)
PhenomicDB: PRDX6

Mutations for PRDX6
* 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 PRDX6 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CA439640PRDX69851173457354173457430PRDX6811371173457113173457460
BG208010MGST21564140661367140661422PRDX6532551173450488173454567
BM477858PRDX614901173454581173457150PPP1R847549412816731228167331
BF972933GRID2567549412300794123026PRDX6604311173455450173457154

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=19)
Stat. for Synonymous SNVs
(# total SNVs=3)
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
chr1:173454533-173454533p.E96*3
chr1:173454569-173454569p.R108W2
chr1:173455475-173455475p.L161I1
chr1:173446625-173446625p.G30E1
chr1:173454570-173454570p.R108Q1
chr1:173455480-173455480p.R162S1
chr1:173450482-173450482p.S38F1
chr1:173454603-173454603p.P119L1
chr1:173455496-173455496p.Q168*1
chr1:173450563-173450563p.N65I1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample2  4  1 1  33   41 3
# mutation2  4  1 1  33   41 3
nonsynonymous SNV2  3  1 1  32   41 3
synonymous SNV   1        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])

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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
chr1:173455423p.S38F1
chr1:173450482p.F202Y1
chr1:173455445p.P45Q1
chr1:173450503p.P203Q1
chr1:173455466p.D85Y1
chr1:173454500p.V206F1
chr1:173455471p.P94P1
chr1:173454529p.R219H1
chr1:173455474p.D105G1
chr1:173454561p.R106M1

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 PRDX6 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 PRDX6

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

ACBD6,COA6,CACYBP,CCDC58,CCT3,GLRX2,HAX1,
JTB,KRTCAP2,PFDN2,PIGC,PRDX6,PSMB4,PSMD4,
RFWD2,SCNM1,SHFM1,SNRPC,SNRPE,THOC7,UCK2
ACAA2,BNIP3,FAM213A,PQLC2L,CIDEC,EIF4EBP2,FAM89A,
FBXO27,GBE1,GHR,GNAI1,HADH,HRSP12,MAOA,
MARC1,PLA2G16,PPARG,PPP1R1A,PRDX6,STBD1,EMC3

ALPI,C11orf86,LINC00520,C1orf94,CAPN11,CIDEC,CLCA4,
CLDN23,CTSE,DHRS9,FAM25BP,GDPD2,GDPD3,GUCA2B,
LOC646627,MYPN,PRDX6,TFF1,UGT1A4,UGT1A5,VSIG1
AMACR,CACFD1,CAPN2,CNNM4,FXYD3,KRTAP5-5,LIPH,
LITAF,LOC646627,LSR,MARCH3,MMP24,MUC20,PEX26,
PIGZ,PLCD3,PRDX6,RIMKLA,SERINC2,TMPRSS4,TSPAN7
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 PRDX6
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
DB03661peroxiredoxin 6experimentalCysteinesulfonic Acid


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Cross referenced IDs for PRDX6
* 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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