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 RAP1B
Basic gene info.Gene symbolRAP1B
Gene nameRAP1B, member of RAS oncogene family
SynonymsK-REV|RAL1B
CytomapUCSC genome browser: 12q14
Genomic locationchr12 :69004618-69054385
Type of geneprotein-coding
RefGenesNM_001010942.2,
NM_001251917.1,NM_001251918.1,NM_001251921.1,NM_001251922.1,
NM_015646.5,
Ensembl idENSG00000127314
DescriptionGTP-binding protein smg p21BRAS-related protein RAP1BRas family small GTP binding protein RAP1Bras-related protein Rap-1bsmall GTP binding protein
Modification date20141207
dbXrefs MIM : 179530
HGNC : HGNC
Ensembl : ENSG00000127314
HPRD : 01546
Vega : OTTHUMG00000133660
ProteinUniProt: P61224
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RAP1B
BioGPS: 5908
Gene Expression Atlas: ENSG00000127314
The Human Protein Atlas: ENSG00000127314
PathwayNCI Pathway Interaction Database: RAP1B
KEGG: RAP1B
REACTOME: RAP1B
ConsensusPathDB
Pathway Commons: RAP1B
MetabolismMetaCyc: RAP1B
HUMANCyc: RAP1B
RegulationEnsembl's Regulation: ENSG00000127314
miRBase: chr12 :69,004,618-69,054,385
TargetScan: NM_001010942
cisRED: ENSG00000127314
ContextiHOP: RAP1B
cancer metabolism search in PubMed: RAP1B
UCL Cancer Institute: RAP1B
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for RAP1B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RAP1B
Familial Cancer Database: RAP1B
* 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_INTEGRATION_OF_ENERGY_METABOLISM

check002.gifOthers
OMIM 179530; gene.
179530; gene.
Orphanet
DiseaseKEGG Disease: RAP1B
MedGen: RAP1B (Human Medical Genetics with Condition)
ClinVar: RAP1B
PhenotypeMGI: RAP1B (International Mouse Phenotyping Consortium)
PhenomicDB: RAP1B

Mutations for RAP1B
* 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 RAP1B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CB243131TLCD27981716083271608418RAP1B94165126902055669020646
CA428502RAP1B158126902057369020632HUWE155180X5356582553565950
BC057387LSM14B12629206069751760704636RAP1B26212685126902055569020638
BF327763RAP1B18101126903211869032201TUBGCP39918113113193332113193414

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 # sample28      3 1  21 1
GAIN (# sample)28      3 1  21 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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=16)
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
chr12:69042539-69042539p.G12E3
chr12:69044198-69044198p.G26*1
chr12:69048013-69048013p.R102Q1
chr12:69042518-69042518p.K5R1
chr12:69044218-69044218p.Y32Y1
chr12:69050104-69050104p.G115C1
chr12:69042529-69042529p.L9F1
chr12:69044223-69044223p.P34H1
chr12:69050130-69050130p.E123E1
chr12:69042538-69042538p.G12R1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample2  2  1 3 131    6 4
# mutation2  2  1 3 131    6 4
nonsynonymous SNV2  2  1 2 121    6 1
synonymous SNV        1  1       3
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
chr12:69042539p.G12E,RAP1B3
chr12:69045809p.R121R,RAP1B1
chr12:69042518p.E3G,RAP1B1
chr12:69047922p.G131V,RAP1B1
chr12:69047944p.K5R,RAP1B1
chr12:69042542p.R134H,RAP1B1
chr12:69048013p.L142F,RAP1B1
chr12:69042543p.G13D,RAP1B1
chr12:69050104p.G13G,RAP1B1
chr12:69042552p.K16K,RAP1B1

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 RAP1B 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 RAP1B

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

CAND1,CCT2,CNOT2,CPSF6,DYRK2,FRS2,GNS,
LEMD3,LLPH,MDM1,MDM2,NUP107,RAB21,RAB3IP,
RAP1B,SLC35E3,TBC1D15,TBK1,TMBIM4,TMEM19,YEATS4
AIDA,AP3S1,ARL2BP,C4orf3,CCNY,CD58,GNG10,
ITM2B,JAZF1,OSTM1,PPP2R3C,RAB1A,RAP1A,RAP1B,
SDCBP,SEPT7,SNX6,STX2,TMEM126B,UBE2E2,VAMP7

ARL1,ARL6IP5,ARPC3,GSKIP,CALM2,CDC42,CNIH1,
DPH3,FAM118B,GOLT1B,HIGD1A,IFNGR1,RAB18,RAP1B,
SAR1B,SELT,TMEM165,TWF1,UBE2D3,USP15,VPS29
ACTR10,ATP5J,BCAS2,C18orf32,CALM2,CDC42,LSM1,
MOB4,NDUFV2,PDCD10,PSMC6,RAB18,RAP1B,SRP14,
SUB1,TXNDC9,UBA3,UBE2F,VPS29,ZFAND6,ZNF410
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 RAP1B


There's no related Drug.
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Cross referenced IDs for RAP1B
* 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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