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 CBR3
Basic gene info.Gene symbolCBR3
Gene namecarbonyl reductase 3
SynonymsHEL-S-25|SDR21C2|hCBR3
CytomapUCSC genome browser: 21q22.2
Genomic locationchr21 :37507262-37518860
Type of geneprotein-coding
RefGenesNM_001236.3,
Ensembl idENSG00000159231
DescriptionNADPH-dependent carbonyl reductase 3carbonyl reductase (NADPH) 3carbonyl reductase [NADPH] 3epididymis secretory protein Li 25short chain dehydrogenase/reductase family 21C, member 2
Modification date20141207
dbXrefs MIM : 603608
HGNC : HGNC
Ensembl : ENSG00000159231
HPRD : 07222
Vega : OTTHUMG00000086617
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CBR3
BioGPS: 874
Gene Expression Atlas: ENSG00000159231
The Human Protein Atlas: ENSG00000159231
PathwayNCI Pathway Interaction Database: CBR3
KEGG: CBR3
REACTOME: CBR3
ConsensusPathDB
Pathway Commons: CBR3
MetabolismMetaCyc: CBR3
HUMANCyc: CBR3
RegulationEnsembl's Regulation: ENSG00000159231
miRBase: chr21 :37,507,262-37,518,860
TargetScan: NM_001236
cisRED: ENSG00000159231
ContextiHOP: CBR3
cancer metabolism search in PubMed: CBR3
UCL Cancer Institute: CBR3
Assigned class in ccmGDBC

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Phenotypic Information for CBR3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CBR3
Familial Cancer Database: CBR3
* 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_ARACHIDONIC_ACID_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: CBR3
MedGen: CBR3 (Human Medical Genetics with Condition)
ClinVar: CBR3
PhenotypeMGI: CBR3 (International Mouse Phenotyping Consortium)
PhenomicDB: CBR3

Mutations for CBR3
* 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 CBR3 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 # sample1                
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=8

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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=7)
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
chr21:37507501-37507501p.C4Y8
chr21:37518706-37518706p.V244M2
chr21:37518377-37518377p.R134I1
chr21:37507593-37507593p.L35F1
chr21:37518441-37518441p.Q155H1
chr21:37507646-37507646p.A52A1
chr21:37518507-37518507p.E177D1
chr21:37507718-37507718p.F76F1
chr21:37518576-37518576p.G200G1
chr21:37507740-37507740p.L84V1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   1  1 1  1    1312
# mutation   1  1 1  1    1312
nonsynonymous SNV      1         13 2
synonymous SNV   1    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
chr21:37507593p.S30F1
chr21:37507764p.V34A1
chr21:37507778p.L35F1
chr21:37510183p.A92T1
chr21:37510203p.K96K1
chr21:37510214p.A117V1
chr21:37518377p.E124K1
chr21:37518591p.P127P1
chr21:37518618p.R134I1
chr21:37507579p.S205S1

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 CBR3 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 CBR3

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

ATP5J2,ATP5J,ATP5O,BTBD6,BUD31,SMCO4,SLIRP,
C19orf43,CBR3,CCDC107,COX6B1,COX7B,DTX2,HEBP2,
LGALS3,PSMC1,PSMG3,SHFM1,TMSB10,U2AF1,ZFAND2B
CBR3,CCDC23,CCM2,CD63,CHMP4A,CLIC1,CLTA,
FAM32A,FAM50A,GMFG,MYL6,NEDD8,NUDT1,RAB13,
ROM1,S100A13,SHFM1,SLC27A3,SNF8,TMSB10,VKORC1

BAK1,SLC18B1,CBR3,CCDC109B,CDC42EP1,CYB5R2,HMSD,
IFI35,JAK2,LMNA,MAP3K6,MPDU1,NANS,NMI,
PSMB6,RTP4,TREX1,UBE2L6,USP18,WDR25,ZMYND15
B3GALNT1,BLVRA,C10orf107,FAM229B,CALCB,CBR3,COX7A1,
FAM133A,FAM195B,GNB4,IL33,KCNMB2,LOC653653,LRRC4C,
NGB,PHKG1,S100B,SNCA,TMEM155,VAMP5,WNT16
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 CBR3
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
DB00694carbonyl reductase 3approvedDaunorubicin
DB00997carbonyl reductase 3approved; investigationalDoxorubicin
DB00445carbonyl reductase 3approvedEpirubicin


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Cross referenced IDs for CBR3
* 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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