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 RAP1A
Basic gene info.Gene symbolRAP1A
Gene nameRAP1A, member of RAS oncogene family
SynonymsC21KG|G-22K|KREV-1|KREV1|RAP1|SMGP21
CytomapUCSC genome browser: 1p13.3
Genomic locationchr1 :112162404-112256101
Type of geneprotein-coding
RefGenesNM_001010935.2,
NM_001291896.1,NM_002884.3,
Ensembl idENSG00000116473
DescriptionGTP-binding protein smg p21ARas-related protein Krev-1ras-related protein Rap-1A
Modification date20141207
dbXrefs MIM : 179520
HGNC : HGNC
HPRD : 01545
ProteinUniProt: P62834
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RAP1A
BioGPS: 5906
Gene Expression Atlas: ENSG00000116473
The Human Protein Atlas: ENSG00000116473
PathwayNCI Pathway Interaction Database: RAP1A
KEGG: RAP1A
REACTOME: RAP1A
ConsensusPathDB
Pathway Commons: RAP1A
MetabolismMetaCyc: RAP1A
HUMANCyc: RAP1A
RegulationEnsembl's Regulation: ENSG00000116473
miRBase: chr1 :112,162,404-112,256,101
TargetScan: NM_001010935
cisRED: ENSG00000116473
ContextiHOP: RAP1A
cancer metabolism search in PubMed: RAP1A
UCL Cancer Institute: RAP1A
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for RAP1A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RAP1A
Familial Cancer Database: RAP1A
* 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 179520; gene.
Orphanet
DiseaseKEGG Disease: RAP1A
MedGen: RAP1A (Human Medical Genetics with Condition)
ClinVar: RAP1A
PhenotypeMGI: RAP1A (International Mouse Phenotyping Consortium)
PhenomicDB: RAP1A

Mutations for RAP1A
* 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 RAP1A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CR997446RAP1A1721112162464112162535EIF4A371607177811386578120850
AA525220RAP1A401241112255650112255734RAP1A1121931112255573112255654
AI207431TRAM1121687151608171516296RAP1A2096731112255277112255741
AA525882RAP1A8921112255650112255734RAP1A801611112255573112255654
BF948052PCDH7926443114431531144576RAP1A2555961112237972112247049
BF329177RAP1A101281112203562112203680SEL1L114360148196475781969115
BP418289RAP1A1281112196355112196382RAP1A221781112196374112196530
AK098133RAP1A15191112193133112193650EIF4G151823223184045905184052842

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   1      
GAIN (# sample)          1      
LOSS (# sample)      1          
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=16)		Stat. for Synonymous SNVs
(# total SNVs=0)
There's no s-snv.
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
chr1:112246984-112246984p.G115D2
chr1:112240096-112240096p.E54K2
chr1:112251778-112251778p.Y159C2
chr1:112238020-112238020p.S39P1
chr1:112246966-112246966p.V109A1
chr1:112238021-112238021p.S39F1
chr1:112246968-112246968p.P110S1
chr1:112240072-112240072p.V46I1
chr1:112246973-112246973p.M111I1
chr1:112240080-112240080p.C48C1

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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
# sample1  2       21   32 2
# mutation1  2       21   32 2
nonsynonymous SNV1  2       21   22 2
synonymous SNV                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
chr1:112246984p.G115D,RAP1A2
chr1:112246033p.T89M,RAP1A1
chr1:112246040p.P110S,RAP1A1
chr1:112246968p.M111I,RAP1A1
chr1:112246973p.K5N,RAP1A1
chr1:112233997p.S11L,RAP1A1
chr1:112234014p.P34Q,RAP1A1
chr1:112238006p.S39P,RAP1A1
chr1:112238020p.S39F,RAP1A1
chr1:112238021p.C48C,RAP1A1

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 RAP1A 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 RAP1A

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

CAPZA1,CD53,CXorf21,CYBB,EVI2A,EVI2B,FYB,
GNAI3,GPR65,LCP2,MDFIC,PLEK,RAB8B,RAP1A,
RGS18,SAMSN1,SGTB,SLC30A7,ST8SIA4,TFEC,WIPF1		AIDA,AP3S1,ARL2BP,CCNY,CD58,COMMD8,EID1,
GNG10,HSD17B11,ITM2B,JAZF1,MORF4L1,PPP2R3C,RAP1A,
RAP1B,RRAS2,SDCBP,SEPT7,SNX3,TMEM126B,VPS29

CFL2,DR1,MICU3,FBXL5,GNAI3,LRCH2,MBNL1,
NEGR1,P2RY14,PALLD,PDE5A,PIGK,PLN,PPAP2A,
RAP1A,RNF11,SH3GLB1,SLC8A1,STX12,STXBP3,TMEM167B		AP1S2,ARPP19,C11orf74,AARD,CCDC91,CETN2,CFL2,
DPT,DSTN,EID1,GYG1,LAPTM4A,MORF4L1,MYL6,
PAIP2,PKIG,RAP1A,SEPT10,SEPT7,SH3BGRL,TCEAL7
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 RAP1A


There's no related Drug.
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Cross referenced IDs for RAP1A
* 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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