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 BLVRB
Basic gene info.Gene symbolBLVRB
Gene namebiliverdin reductase B
SynonymsBVRB|FLR|HEL-S-10|SDR43U1
CytomapUCSC genome browser: 19q13.1-q13.2
Genomic locationchr19 :40953690-40971725
Type of geneprotein-coding
RefGenesNM_000713.2,
Ensembl idENSG00000090013
DescriptionBVR-BFRGHBPNADPH-dependent diaphoraseNADPH-flavin reductasebiliverdin reductase B (flavin reductase (NADPH))biliverdin-IX beta-reductaseepididymis secretory protein Li 10flavin reductase (NADPH)green heme-binding proteinshort chain dehydrogenase
Modification date20141207
dbXrefs MIM : 600941
HGNC : HGNC
Ensembl : ENSG00000090013
HPRD : 02967
Vega : OTTHUMG00000182593
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_BLVRB
BioGPS: 645
Gene Expression Atlas: ENSG00000090013
The Human Protein Atlas: ENSG00000090013
PathwayNCI Pathway Interaction Database: BLVRB
KEGG: BLVRB
REACTOME: BLVRB
ConsensusPathDB
Pathway Commons: BLVRB
MetabolismMetaCyc: BLVRB
HUMANCyc: BLVRB
RegulationEnsembl's Regulation: ENSG00000090013
miRBase: chr19 :40,953,690-40,971,725
TargetScan: NM_000713
cisRED: ENSG00000090013
ContextiHOP: BLVRB
cancer metabolism search in PubMed: BLVRB
UCL Cancer Institute: BLVRB
Assigned class in ccmGDBC

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

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

Mutations for BLVRB
* 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
pancreasBLVRBchr194096359040963610BLVRBchr194096463940964659
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 BLVRB 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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample        1        
GAIN (# sample)        1        
LOSS (# sample)                 
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=4)
Stat. for Synonymous SNVs
(# total SNVs=6)
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
chr19:40953835-40953835p.Y194Y2
chr19:40964105-40964105p.A97A1
chr19:40964286-40964286p.?1
chr19:40964289-40964289p.L81L1
chr19:40964325-40964325p.D69D1
chr19:40953837-40953837p.Y194H1
chr19:40964360-40964360p.A58T1
chr19:40953902-40953902p.P172L1
chr19:40957295-40957295p.V147M1
chr19:40957334-40957334p.R134W1

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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 1 4  1    11   1  1
# mutation 1 4  1    11   1  1
nonsynonymous SNV 1 2       1    1   
synonymous SNV   2  1     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
chr19:40953835p.Y194Y2
chr19:40964360p.P172H1
chr19:40971542p.R134W1
chr19:40953902p.D131N1
chr19:40957334p.A127S1
chr19:40957343p.L114L1
chr19:40957355p.L81L1
chr19:40957392p.A58T1
chr19:40964289p.T18T1

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 BLVRB 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 BLVRB

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

ATOX1,BLVRB,COX14,HYPK,CHMP2A,DCXR,DDRGK1,
DHRS4,GAMT,GPX4,MRPL41,NDUFA2,NDUFB10,RAB4B,
SDSL,SERTAD3,SIL1,SURF1,TMEM141,TRAPPC6A,UQCR11
ARL2,ASCC2,BLOC1S1,BLVRB,CNPPD1,CCM2,CD63,
FAM50A,IFI27L1,LOC729991,MRPS11,NAGLU,NUCB1,OAZ1,
POLD4,POLR2L,RNH1,RNPEPL1,SMPD1,UROD,USF2

BLVRB,SMCO4,C12orf57,C19orf33,CYSTM1,CDC42EP5,ECI1,
ETHE1,FAM98C,NAA38,MED11,NPAS1,PSMD8,RILP,
S100P,SAT2,SERTAD1,TSPAN15,TSPO,TTC9B,YIF1B
AP2S1,ARF5,ATP6V0E1,BLOC1S1,BLVRB,LAMTOR1,UQCC3,
MIEN1,CHCHD5,DAD1,JAGN1,MRPS11,NDUFA13,NDUFA2,
OAZ1,POP4,NELFE,SDF2,UBL5,WIBG,ZNHIT1
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 BLVRB
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
DB00140biliverdin reductase B (flavin reductase (NADPH))approved; nutraceuticalRiboflavin
DB00157biliverdin reductase B (flavin reductase (NADPH))approved; nutraceuticalNADH
DB02073biliverdin reductase B (flavin reductase (NADPH))experimentalBiliverdine Ix Alpha
DB03247biliverdin reductase B (flavin reductase (NADPH))experimentalRiboflavin Monophosphate
DB03461biliverdin reductase B (flavin reductase (NADPH))experimental2'-Monophosphoadenosine 5'-Diphosphoribose
DB04345biliverdin reductase B (flavin reductase (NADPH))experimental7,8-dimethylalloxazine
DB04363biliverdin reductase B (flavin reductase (NADPH))experimentalMesobiliverdin Iv Alpha
DB00987biliverdin reductase B (flavin reductase (NADPH))approved; investigationalCytarabine


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Cross referenced IDs for BLVRB
* 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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