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 PEX11A
Basic gene info.Gene symbolPEX11A
Gene nameperoxisomal biogenesis factor 11 alpha
SynonymsPEX11-ALPHA|PMP28|hsPEX11p
CytomapUCSC genome browser: 15q26.1
Genomic locationchr15 :90226286-90233958
Type of geneprotein-coding
RefGenesNM_001271572.1,
NM_001271573.1,NM_003847.2,
Ensembl idENSG00000166821
Description28 kDa peroxisomal integral membrane proteinperoxin-11Aperoxisomal biogenesis factor 11Aperoxisomal membrane protein 11Aprotein PEX11 homolog alpha
Modification date20141207
dbXrefs MIM : 603866
HGNC : HGNC
Ensembl : ENSG00000166821
HPRD : 04843
Vega : OTTHUMG00000149809
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PEX11A
BioGPS: 8800
Gene Expression Atlas: ENSG00000166821
The Human Protein Atlas: ENSG00000166821
PathwayNCI Pathway Interaction Database: PEX11A
KEGG: PEX11A
REACTOME: PEX11A
ConsensusPathDB
Pathway Commons: PEX11A
MetabolismMetaCyc: PEX11A
HUMANCyc: PEX11A
RegulationEnsembl's Regulation: ENSG00000166821
miRBase: chr15 :90,226,286-90,233,958
TargetScan: NM_001271572
cisRED: ENSG00000166821
ContextiHOP: PEX11A
cancer metabolism search in PubMed: PEX11A
UCL Cancer Institute: PEX11A
Assigned class in ccmGDBC

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Phenotypic Information for PEX11A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PEX11A
Familial Cancer Database: PEX11A
* 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

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PEX11A
MedGen: PEX11A (Human Medical Genetics with Condition)
ClinVar: PEX11A
PhenotypeMGI: PEX11A (International Mouse Phenotyping Consortium)
PhenomicDB: PEX11A

Mutations for PEX11A
* 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 PEX11A 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

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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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=15)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr15:90226613-90226613p.R247C2
chr15:90226620-90226620p.L244L2
chr15:90226656-90226656p.A232A2
chr15:90226684-90226684p.G223E2
chr15:90226610-90226610p.*248E1
chr15:90226809-90226809p.L181L1
chr15:90226990-90226990p.T121M1
chr15:90226823-90226823p.L177F1
chr15:90227003-90227003p.E117*1
chr15:90226836-90226836p.E172D1

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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
# sample   32 4    5 1  22 5
# mutation   32 4    5 1  23 5
nonsynonymous SNV   11 4    4 1  22 5
synonymous SNV   21      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
chr15:90226613p.R102S,PEX11A2
chr15:90226612p.I64F,PEX11A1
chr15:90226924p.R102H,PEX11A1
chr15:90229663p.R62H,PEX11A1
chr15:90226942p.L99L,PEX11A1
chr15:90229763p.R83H1
chr15:90226620p.M89I,PEX11A1
chr15:90226986p.T78I1
chr15:90226650p.A87A,PEX11A1
chr15:90226989p.V64V1

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 PEX11A 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 PEX11A

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

AP3S2,ARPIN,GDPGP1,CA12,CIB1,FAM174B,GPD1L,
HSDL2,IDH2,LINS,MPP7,NGRN,PEX11A,RALGPS2,
RBM47,SEMA4B,SPOPL,THUMPD1,WDR93,ZSCAN32,ZNF823
ABHD15,ACSS3,ACVR1C,ADIPOQ,AQPEP,BNIP3L,FAM219B,
CABLES1,GPATCH11,EPB41L4B,GHR,IDH1,OXCT1,PCCA,
PDP2,PECR,PEX11A,PEX19,SLC19A3,TBC1D20,TJP2

SOWAHB,C10orf99,C1orf210,CALML4,CAT,EHHADH,EPB41L4B,
ETFA,FAM134B,GPA33,GPD1L,LRRC19,NAT2,OMA1,
PEX11A,PPARG,SGK2,SLC16A9,SLC9A2,SULT1B1,TTC38
ABHD5,ADH1C,AP3S2,AUH,BTBD3,PPP1R36,SAYSD1,
CHPT1,EHHADH,ETFDH,FAM45A,HSD17B2,IDH1,NAT2,
NRG4,PAFAH2,PEX11A,SNX14,TMEM38B,UGT1A10,XK
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 PEX11A


There's no related Drug.
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Cross referenced IDs for PEX11A
* 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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