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 PHAX
Basic gene info.Gene symbolPHAX
Gene namephosphorylated adaptor for RNA export
SynonymsRNUXA
CytomapUCSC genome browser: 5q23.2
Genomic locationchr5 :125936606-125962944
Type of geneprotein-coding
RefGenesNM_032177.3,
Ensembl idENSG00000164902
DescriptionRNA U small nuclear RNA export adapter proteinRNA U, small nuclear RNA export adapter (phosphorylation regulated)RNA U, small nuclear RNA export adaptor (phosphorylation regulated)phosphorylated adapter RNA export protein
Modification date20141207
dbXrefs MIM : 604924
HGNC : HGNC
Ensembl : ENSG00000164902
HPRD : 15122
Vega : OTTHUMG00000163273
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PHAX
BioGPS: 51808
Gene Expression Atlas: ENSG00000164902
The Human Protein Atlas: ENSG00000164902
PathwayNCI Pathway Interaction Database: PHAX
KEGG: PHAX
REACTOME: PHAX
ConsensusPathDB
Pathway Commons: PHAX
MetabolismMetaCyc: PHAX
HUMANCyc: PHAX
RegulationEnsembl's Regulation: ENSG00000164902
miRBase: chr5 :125,936,606-125,962,944
TargetScan: NM_032177
cisRED: ENSG00000164902
ContextiHOP: PHAX
cancer metabolism search in PubMed: PHAX
UCL Cancer Institute: PHAX
Assigned class in ccmGDBC

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

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

Mutations for PHAX
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
prostatePHAXchr5125938600125940600PPP2R1Achr195270486052706860
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 PHAX related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI808197PHAX12855125961633125961916PHAX2835075125961944125962168
AI766928FAM63B10204155911708859117282PHAX2043705125960833125960999

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 # sample1                
GAIN (# sample)                 
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=1

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=17)
Stat. for Synonymous SNVs
(# total SNVs=5)
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
chr5:125939712-125939712p.M185fs*232
chr5:125939530-125939530p.L122Q1
chr5:125960302-125960302p.E317D1
chr5:125936659-125936659p.A2V1
chr5:125939585-125939585p.E140D1
chr5:125960337-125960337p.V329G1
chr5:125936672-125936672p.G6G1
chr5:125960353-125960353p.M334I1
chr5:125936697-125936697p.D15Y1
chr5:125939782-125939782p.R206K1

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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
# sample   7  1 1   21  14 1
# mutation   8  1 1   21  14 1
nonsynonymous SNV   5  1 1   21  12 1
synonymous SNV   3             2  
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
chr5:125952952p.R281Q2
chr5:125939811p.A2V1
chr5:125936659p.M334I1
chr5:125939833p.G6G1
chr5:125936672p.T358T1
chr5:125936697p.D15Y1
chr5:125952978p.E374K1
chr5:125939331p.H56Y1
chr5:125960302p.I393I1
chr5:125939416p.R84P1

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 PHAX 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 PHAX

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

AFF4,AGGF1,APC,C5orf24,CSNK1G3,DDX46,FBXO38,
FBXW11,FNIP1,KDM3B,MATR3,MIER3,PHAX,RAD50,
RBM27,SLC25A46,SMAD5,SRFBP1,TTC37,UTP15,YTHDC2
AHCTF1,ANKIB1,ARID4A,ATRX,ERCC6L2,DIS3,DMXL1,
ESF1,IREB2,ITCH,PHAX,RAB3GAP2,RB1CC1,RPS6KB1,
NEMF,SCAF11,SLK,TRPM7,USP8,ZFR,ZFX

AGGF1,CEP120,CHD1,CNOT6,COL4A3BP,DDX46,DHX29,
DMXL1,ETF1,HSPA4,IPO11,LNPEP,LYSMD3,MATR3,
PGGT1B,PHAX,RBM27,RIOK2,SNX2,WDR36,YTHDC2
ATAD1,C6orf203,CCDC117,CCDC132,GSPT2,HSDL2,IFT74,
MED20,METAP1,MPP7,STK26,MTMR2,NCK1,PCCA,
PHAX,PPID,PTGES3,SDR42E1,UBE2D1,UBE2E1,XRN2
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 PHAX


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