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 BBOX1
Basic gene info.Gene symbolBBOX1
Gene namebutyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 1
SynonymsBBH|BBOX|G-BBH|gamma-BBH
CytomapUCSC genome browser: 11p14.2
Genomic locationchr11 :27062508-27149354
Type of geneprotein-coding
RefGenesNM_003986.2,
Ensembl idENSG00000129151
Descriptiongamma-butyrobetaine dioxygenasegamma-butyrobetaine hydroxylasegamma-butyrobetaine,2-oxoglutarate dioxygenase 1
Modification date20141207
dbXrefs MIM : 603312
HGNC : HGNC
Ensembl : ENSG00000129151
HPRD : 04498
Vega : OTTHUMG00000166121
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_BBOX1
BioGPS: 8424
Gene Expression Atlas: ENSG00000129151
The Human Protein Atlas: ENSG00000129151
PathwayNCI Pathway Interaction Database: BBOX1
KEGG: BBOX1
REACTOME: BBOX1
ConsensusPathDB
Pathway Commons: BBOX1
MetabolismMetaCyc: BBOX1
HUMANCyc: BBOX1
RegulationEnsembl's Regulation: ENSG00000129151
miRBase: chr11 :27,062,508-27,149,354
TargetScan: NM_003986
cisRED: ENSG00000129151
ContextiHOP: BBOX1
cancer metabolism search in PubMed: BBOX1
UCL Cancer Institute: BBOX1
Assigned class in ccmGDBC

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Phenotypic Information for BBOX1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: BBOX1
Familial Cancer Database: BBOX1
* 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_AMINO_ACIDS_AND_DERIVATIVES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: BBOX1
MedGen: BBOX1 (Human Medical Genetics with Condition)
ClinVar: BBOX1
PhenotypeMGI: BBOX1 (International Mouse Phenotyping Consortium)
PhenomicDB: BBOX1

Mutations for BBOX1
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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
ovaryBBOX1chr112706274627062766CD300Echr177261866172618681
ovaryBBOX1chr112712387227123892chr112620703926207059
pancreasBBOX1chr112707286927072889BBOX1chr112707471127074731
pancreasBBOX1chr112708080027080820BBOX1chr112708303927083059
pancreasBBOX1chr112709608627096106BBOX1chr112707477427074794
pancreasBBOX1chr112712296327122983BBOX1chr112712448327124503
pancreasBBOX1chr112712777427127974chr112717755127177751
pancreasBBOX1chr112714198927142009LGR4chr112742589127425911
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 BBOX1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF750399BBOX11196112711398927114184KLK7193305195148370851485099
AW798404BBOX176103112708977127089800FOS101224147574860175748724

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 # sample  1     1        
GAIN (# sample)        1        
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=35)
Stat. for Synonymous SNVs
(# total SNVs=9)
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
chr11:27114788-27114788p.H136H3
chr11:27078827-27078827p.A100D2
chr11:27114906-27114906p.F176V2
chr11:27137012-27137012p.V183M2
chr11:27148884-27148884p.R350C2
chr11:27148982-27148982p.R382R2
chr11:27114883-27114883p.R168K1
chr11:27148986-27148986p.E384K1
chr11:27077154-27077154p.D59E1
chr11:27141378-27141378p.K274K1

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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
# sample21161 2 1  73   63 2
# mutation21251 2 2  73   63 2
nonsynonymous SNV1 24  1 2  62   32 1
synonymous SNV11 11 1    11   31 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
chr11:27148982p.F176V2
chr11:27114906p.R382R2
chr11:27148880p.C113C1
chr11:27078769p.A312D1
chr11:27141369p.E128K1
chr11:27148881p.E325K1
chr11:27078781p.G166W1
chr11:27141378p.G348G1
chr11:27148882p.R349R1
chr11:27078786p.D188H1

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 BBOX1 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 BBOX1

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

ANXA1,BBOX1,CEBPB,CFI,CHI3L1,CNTNAP3,DEFB1,
CCDC71L,GABRP,HAPLN3,LYN,MOB3B,MPZL2,PAK3,
PLCG2,PROM1,RARRES1,TANK,TIGD2,TINAGL1,TLR2
ALDH1A3,ARFGAP3,BBOX1,PLEKHS1,EVA1C,CA13,CDCP1,
CMTM7,CXCL16,GRAMD2,LOC100190939,LRRC4C,LTF,PROM1,
RARRES1,RASGEF1A,SLC34A2,SLPI,STAC2,TC2N,VGLL1

ANGPTL5,BBOX1,C17orf78,CALCB,CLDN22,CYP17A1,CYP7A1,
EPB42,GLIPR1,HSD17B13,INSC,LBP,MRAP,NLRP6,
PTCHD3,SERPINE3,SLC7A9,SPAM1,TAAR1,TBX3,TMEM229A
ACADL,BBOX1,LINC00301,C1orf194,C1QL1,FAM228A,CLPSL2,
SPATA31D1,GLYAT,GTF2A1L,IFNA2,KLHDC8A,MGC2889,OR52D1,
PCDHB18,S100G,SCN1A,TAAR8,TF,USP17L9P,WSCD2
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 BBOX1
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
DB00126butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 1approved; nutraceuticalVitamin C
DB00139butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 1approved; nutraceuticalSuccinic acid
DB00145butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 1approved; nutraceuticalGlycine


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Cross referenced IDs for BBOX1
* 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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