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 PDHX
Basic gene info.Gene symbolPDHX
Gene namepyruvate dehydrogenase complex, component X
SynonymsDLDBP|E3BP|OPDX|PDX1|proX
CytomapUCSC genome browser: 11p13
Genomic locationchr11 :34937676-35017675
Type of geneprotein-coding
RefGenesNM_001135024.1,
NM_001166158.1,NM_003477.2,
Ensembl idENSG00000110435
Descriptiondihydrolipoamide dehydrogenase-binding protein of pyruvate dehydrogenase complexlipoyl-containing pyruvate dehydrogenase complex component Xpyruvate dehydrogenase complex, E3-binding protein subunitpyruvate dehydrogenase complex, lipoyl-containing comp
Modification date20141207
dbXrefs MIM : 608769
HGNC : HGNC
Ensembl : ENSG00000110435
HPRD : 02002
Vega : OTTHUMG00000166491
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDHX
BioGPS: 8050
Gene Expression Atlas: ENSG00000110435
The Human Protein Atlas: ENSG00000110435
PathwayNCI Pathway Interaction Database: PDHX
KEGG: PDHX
REACTOME: PDHX
ConsensusPathDB
Pathway Commons: PDHX
MetabolismMetaCyc: PDHX
HUMANCyc: PDHX
RegulationEnsembl's Regulation: ENSG00000110435
miRBase: chr11 :34,937,676-35,017,675
TargetScan: NM_001135024
cisRED: ENSG00000110435
ContextiHOP: PDHX
cancer metabolism search in PubMed: PDHX
UCL Cancer Institute: PDHX
Assigned class in ccmGDBC

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

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

Mutations for PDHX
* 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
ovaryPDHXchr113501293335012953PDHXchr113497884834978868
ovaryPDHXchr113501554935015569ABTB2chr113423339334233413
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 PDHX related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA471107CD441204113516071835160921PDHX200567113495295034979115
AK024187PDHX1108113498797934988086THRAP396104613672547236726422
AU122517PDHX1108113498797934988086THRAP39677713672547236726149
BQ358867PDHX1238113498198034988339CTDSPL23155233801124538011567
CV360819PDHX20125113495294934969075PDHX122428113499174735006277

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 # sample2     4 2 1   2 2
GAIN (# sample)2     1 2 1   2 1
LOSS (# sample)      3         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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=32)
Stat. for Synonymous SNVs
(# total SNVs=15)
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
chr11:35016492-35016492p.E427*3
chr11:35006231-35006231p.D380Y3
chr11:35016516-35016516p.P435S2
chr11:34988314-34988314p.R257R2
chr11:34978943-34978943p.S119R2
chr11:35016594-35016594p.L461L2
chr11:34991727-34991727p.V286V2
chr11:34969060-34969060p.A83A2
chr11:35016488-35016488p.I425I2
chr11:34981990-34981990p.R189H1

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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
# sample11 3  4 3  431  34 13
# mutation11 4  4 3  431  35 12
nonsynonymous SNV11 3  4 2  411  22 9
synonymous SNV   1    1   2   13 3
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
chr11:35006231p.D153H,PDHX3
chr11:35016488p.I198I,PDHX2
chr11:34978943p.L234L,PDHX2
chr11:35016594p.S104G,PDHX2
chr11:34988233p.G163E,PDHX1
chr11:34979028p.D303Y,PDHX1
chr11:34988250p.L304L,PDHX1
chr11:35006241p.R174G,PDHX1
chr11:34979113p.I317I,PDHX1
chr11:34988314p.R174H,PDHX1

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 PDHX 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 PDHX

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

ABTB2,API5,APIP,ARL14EP,CAPRIN1,CAT,CD44,
CKAP5,COMMD9,CSTF3,FBXO3,LOC283267,MTCH2,NAT10,
NUP160,PDHX,QSER1,SLC1A2,TCP11L1,TRAF6,TRIM44
ACAT1,ALDH5A1,ALPK3,ATP5B,ADCK3,COX10,GYS1,
HADHB,KLHL31,NDUFS1,NNT,NRD1,PDHX,PPP3CB,
RXRG,SCN4A,SDHB,SOX6,UBR3,UQCRFS1,ZYG11B

ABHD10,API5,ATP5B,MIS18A,C2orf47,COPB1,DLAT,
FAR1,KIF18A,LIN7C,MRPL19,MRS2,MTCH2,NDUFS3,
PDHB,PDHX,PSMA1,SAAL1,SDHD,SFXN1,TMX2
ATP5C1,ATP5F1,MPC1,BZW2,TEFM,DLAT,MEMO1,
MRPL35,MRPS28,MRPS30,MRPS33,MRPS35,OXSM,PCCB,
PDHX,SPRYD4,SSX8,STEAP1,UQCRC2,UQCRFS1,WDR12
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 PDHX
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
DB04284pyruvate dehydrogenase complex, component XexperimentalProline Betaine
DB04455pyruvate dehydrogenase complex, component XexperimentalTrimethyl Glycine


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Cross referenced IDs for PDHX
* 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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