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 RENBP
Basic gene info.Gene symbolRENBP
Gene namerenin binding protein
SynonymsRBP|RNBP
CytomapUCSC genome browser: Xq28
Genomic locationchrX :153200721-153210232
Type of geneprotein-coding
RefGenesNM_002910.5,
Ensembl idENSG00000269198
DescriptionAGEGlcNAc 2-epimeraseN-acetyl-D-glucosamine 2-epimeraseN-acylglucosamine 2-epimerase
Modification date20141207
dbXrefs MIM : 312420
HGNC : HGNC
Ensembl : ENSG00000102032
HPRD : 02423
Vega : OTTHUMG00000024224
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RENBP
BioGPS: 5973
Gene Expression Atlas: ENSG00000269198
The Human Protein Atlas: ENSG00000269198
PathwayNCI Pathway Interaction Database: RENBP
KEGG: RENBP
REACTOME: RENBP
ConsensusPathDB
Pathway Commons: RENBP
MetabolismMetaCyc: RENBP
HUMANCyc: RENBP
RegulationEnsembl's Regulation: ENSG00000269198
miRBase: chrX :153,200,721-153,210,232
TargetScan: NM_002910
cisRED: ENSG00000269198
ContextiHOP: RENBP
cancer metabolism search in PubMed: RENBP
UCL Cancer Institute: RENBP
Assigned class in ccmGDBC

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

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

Mutations for RENBP
* 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 RENBP related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF799253RENBP170191X153205691153205712RAD23A180371191305906913059528

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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=26)
Stat. for Synonymous SNVs
(# total SNVs=10)
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
chr23:153206997-153206997p.S283S2
chr23:153208402-153208402p.L188M1
chr23:153209094-153209094p.G112G1
chr23:153205581-153205581p.Q341K1
chr23:153209604-153209604p.G37G1
chr23:153208406-153208406p.L186L1
chr23:153209095-153209095p.G112D1
chr23:153205589-153205589p.L338P1
chr23:153209775-153209775p.H31H1
chr23:153207037-153207037p.A270D1

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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 41 2 2  331  3217
# mutation31 41 2 2  331  4217
nonsynonymous SNV2  31 2 2  321  3115
synonymous SNV11 1        1   11 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
chrX:153209166p.K383K1
chrX:153205589p.D231N1
chrX:153207421p.V25A1
chrX:153209359p.Q351K1
chrX:153205592p.I164I1
chrX:153207423p.E14A1
chrX:153209401p.L348P1
chrX:153205628p.E159A1
chrX:153207433p.R347H1
chrX:153209420p.F136L1

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 RENBP 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 RENBP

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

ANGPTL6,SOWAHD,APOE,BRI3,FUOM,THEMIS2,C1QA,
C1QB,CYBA,DOK2,FERMT3,GPX1,IFI30,NCF4,
RENBP,RHOG,SPI1,IGFLR1,TNFRSF4,TYMP,TYROBP
C1QA,TOR4A,CD68,CTSL,CTSZ,DOK2,FCGRT,
FOLR2,FTL,COLGALT1,IFFO1,LOXL3,NRROS,MCOLN1,
MGAT1,MPP1,NCF4,RENBP,SPI1,TCN2,TRPV2

ACP5,ADPRH,C1orf85,CECR1,CPVL,CTSH,CTSZ,
CYB5R1,FGD3,GBGT1,HSD17B14,KCNAB2,KLHDC8B,NPL,
PLA1A,RENBP,SCPEP1,SLC47A1,TFE3,TMEM86A,TPP1
ARRB2,C1QA,C1QB,C1QC,C2,C3AR1,CD33,
CMKLR1,CSF1R,GGTA1P,HK3,HSD17B14,LAIR1,LRRC25,
MAFB,PILRA,RASGRP4,RENBP,SCPEP1,SIGLEC1,SLC24A4
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 RENBP
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
DB00141renin binding proteinapproved; nutraceuticalN-Acetyl-D-glucosamine


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Cross referenced IDs for RENBP
* 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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