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 BPNT1
Basic gene info.Gene symbolBPNT1
Gene name3'(2'), 5'-bisphosphate nucleotidase 1
SynonymsHEL20|PIP
CytomapUCSC genome browser: 1q41
Genomic locationchr1 :220230823-220263191
Type of geneprotein-coding
RefGenesNM_001286149.1,
NM_001286150.1,NM_001286151.1,NM_006085.5,
Ensembl idENSG00000162813
Description3'(2'),5'-bisphosphate nucleotidase 1BPntasePAP-inositol 1,4-phosphatasePAP-inositol-1,4-phosphatasebisphosphate 3'-nucleotidase 1epididymis luminal protein 20
Modification date20141207
dbXrefs MIM : 604053
HGNC : HGNC
Ensembl : ENSG00000162813
HPRD : 06814
Vega : OTTHUMG00000037435
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_BPNT1
BioGPS: 10380
Gene Expression Atlas: ENSG00000162813
The Human Protein Atlas: ENSG00000162813
PathwayNCI Pathway Interaction Database: BPNT1
KEGG: BPNT1
REACTOME: BPNT1
ConsensusPathDB
Pathway Commons: BPNT1
MetabolismMetaCyc: BPNT1
HUMANCyc: BPNT1
RegulationEnsembl's Regulation: ENSG00000162813
miRBase: chr1 :220,230,823-220,263,191
TargetScan: NM_001286149
cisRED: ENSG00000162813
ContextiHOP: BPNT1
cancer metabolism search in PubMed: BPNT1
UCL Cancer Institute: BPNT1
Assigned class in ccmGDBC

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Phenotypic Information for BPNT1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: BPNT1
Familial Cancer Database: BPNT1
* 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_SULFUR_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: BPNT1
MedGen: BPNT1 (Human Medical Genetics with Condition)
ClinVar: BPNT1
PhenotypeMGI: BPNT1 (International Mouse Phenotyping Consortium)
PhenomicDB: BPNT1

Mutations for BPNT1
* 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 BPNT1 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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=28)
Stat. for Synonymous SNVs
(# total SNVs=6)
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
chr1:220236249-220236249p.G174G2
chr1:220247379-220247379p.R52Q2
chr1:220253146-220253146p.A15T2
chr1:220240690-220240690p.G143E2
chr1:220246300-220246300p.?2
chr1:220240718-220240718p.T134S2
chr1:220232232-220232232p.Y294F1
chr1:220247344-220247344p.R64W1
chr1:220242756-220242756p.P118S1
chr1:220232313-220232314p.G267L1

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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
# sample21 5  1  1 6211 13 3
# mutation21 4  1  1 8211 13 3
nonsynonymous SNV21 4  1  1 411   2 3
synonymous SNV           41 1 11  
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
chr1:220247379p.R52Q,BPNT12
chr1:220232232p.Y238C,BPNT11
chr1:220240716p.A51G,BPNT11
chr1:220232235p.H211R,BPNT11
chr1:220240733p.V27V,BPNT11
chr1:220253107p.D209N,BPNT11
chr1:220232316p.L22M,BPNT11
chr1:220242730p.V203V,BPNT11
chr1:220253139p.R9R,BPNT11
chr1:220232323p.A202D,BPNT11

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 BPNT1 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 BPNT1

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

ADSS,AHCTF1,BPNT1,DIEXF,SPRTN,C1orf131,CDC73,
EPRS,FBXO28,GNPAT,IARS2,INTS7,IPO9,NUP133,
RAB3GAP2,RPS6KC1,RRP15,SNAP47,TAF5L,TFB2M,TIMM17A
ADSS,ARMCX5,BPNT1,CCDC138,CDC42SE1,DNAH14,E2F5,
FAM60A,GDPD1,HOOK1,IFT74,MSH2,OAT,PI4K2B,
RFC3,SRSF6,STRBP,TC2N,TDG,TDP1,VHL

APH1A,ARPC5,BLZF1,BPNT1,C1orf43,COG2,GOLPH3L,
MRPS14,PEX19,RAB25,RAB4A,RABIF,RFWD2,SDHC,
TAF5L,TFB2M,TIPRL,TMCO1,TMEM183A,TPM3,TSNAX
BPNT1,ABRACL,CRYL1,ETFA,RMDN2,HDHD3,HTATIP2,
LGALS3,MAD2L1BP,MGST3,MLX,MYL12B,NAT2,NDFIP2,
NMNAT1,SLC51B,SLC25A20,SLC25A5,SLMO2,SRI,TACO1
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 BPNT1


There's no related Drug.
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Cross referenced IDs for BPNT1
* 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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