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 RBP2
Basic gene info.Gene symbolRBP2
Gene nameretinol binding protein 2, cellular
SynonymsCRABP-II|CRBP2|CRBPII|RBPC2
CytomapUCSC genome browser: 3q23
Genomic locationchr3 :139171725-139195352
Type of geneprotein-coding
RefGenesNM_004164.2,
Ensembl idENSG00000114113
DescriptionCRBP-IIcellular retinol-binding protein IIretinol-binding protein 2retinol-binding protein 2, cellular
Modification date20141222
dbXrefs MIM : 180280
HGNC : HGNC
Ensembl : ENSG00000114113
HPRD : 07184
Vega : OTTHUMG00000159956
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RBP2
BioGPS: 5948
Gene Expression Atlas: ENSG00000114113
The Human Protein Atlas: ENSG00000114113
PathwayNCI Pathway Interaction Database: RBP2
KEGG: RBP2
REACTOME: RBP2
ConsensusPathDB
Pathway Commons: RBP2
MetabolismMetaCyc: RBP2
HUMANCyc: RBP2
RegulationEnsembl's Regulation: ENSG00000114113
miRBase: chr3 :139,171,725-139,195,352
TargetScan: NM_004164
cisRED: ENSG00000114113
ContextiHOP: RBP2
cancer metabolism search in PubMed: RBP2
UCL Cancer Institute: RBP2
Assigned class in ccmGDBC

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Phenotypic Information for RBP2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RBP2
Familial Cancer Database: RBP2
* 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_STEROID_HORMONES_AND_VITAMINS_A_AND_D
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: RBP2
MedGen: RBP2 (Human Medical Genetics with Condition)
ClinVar: RBP2
PhenotypeMGI: RBP2 (International Mouse Phenotyping Consortium)
PhenomicDB: RBP2

Mutations for RBP2
* 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 RBP2 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     11 
GAIN (# sample)        1     11 
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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=13)
Stat. for Synonymous SNVs
(# total SNVs=5)
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
chr3:139181131-139181131p.D25E2
chr3:139195259-139195259p.E15K1
chr3:139173596-139173596p.W110*1
chr3:139181108-139181108p.I33T1
chr3:139195274-139195274p.E10K1
chr3:139173610-139173610p.R105R1
chr3:139181123-139181123p.F28S1
chr3:139195275-139195275p.W9*1
chr3:139173612-139173612p.R105C1
chr3:139181127-139181127p.D27N1

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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
# sample1  11      72   21 3
# mutation1  11      72   21 3
nonsynonymous SNV1  11      51   2  1
synonymous SNV           21    1 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
chr3:139173626p.D92E1
chr3:139195245p.R81Q1
chr3:139173634p.R36C1
chr3:139195249p.V35E1
chr3:139173649p.I33T1
chr3:139180964p.F28S1
chr3:139181100p.D27N1
chr3:139181102p.I26T1
chr3:139172003p.A23S1
chr3:139181108p.L120L1

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 RBP2 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 RBP2

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

C4BPB,TMEM244,CTNNA2,DNASE2B,DPCR1,HSCB,KRTAP10-8,
LOC360030,MRPL2,NIPSNAP1,NUDT11,OR2W5,PGC,RBP2,
SLC17A3,SPINT3,SULT1B1,THOC5,TOMM6,UNC5D,ZNF689
ATG16L1,CASC1,CCDC30,FAM226B,DCDC1,FLJ22536,HKR1,
MAGEB2,METTL16,OR5D16,PDXDC2P,PLEKHM1P,PPFIBP2,PRB3,
RBP2,SCARNA10,SCARNA1,SCARNA5,SH2D6,SLC23A1,ZNF433

C1orf158,UMODL1-AS1,LINC00575,C5orf49,CCL25,CDC20B,CEBPA,
CPB2,DAB1,LOC100287718,LPO,LRRC43,MYBPHL,RBP2,
SERPINA7,SLC13A2,SLC23A1,SLC7A9,SNORA11E,SOAT2,TEKT1
APOB,APOC3,C17orf78,CEACAM20,CRISP1,FABP6,FAM99A,
FAM99B,GSTA2,GSTA5,LCE3E,LOC388428,MOS,ONECUT3,
OR10H1,OR10H5,OR4N5,PWAR4___F2RL3___PAWR,RBP2,SLC5A12,SPANXN3
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 RBP2


There's no related Drug.
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Cross referenced IDs for RBP2
* 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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