Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 symbol	RAP1A
	Gene name	RAP1A, member of RAS oncogene family
	Synonyms	C21KG\|G-22K\|KREV-1\|KREV1\|RAP1\|SMGP21
	Cytomap	UCSC genome browser: 1p13.3
	Genomic location	chr1 :112162404-112256101
	Type of gene	protein-coding
	RefGenes	NM_001010935.2, NM_001291896.1,NM_002884.3,
	Ensembl id	ENSG00000116473
	Description	GTP-binding protein smg p21ARas-related protein Krev-1ras-related protein Rap-1A
	Modification date	20141207
dbXrefs	MIM : 179520
	HGNC : HGNC
	HPRD : 01545
Protein	UniProt: P62834 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RAP1A
	BioGPS: 5906
	Gene Expression Atlas: ENSG00000116473
	The Human Protein Atlas: ENSG00000116473
Pathway	NCI Pathway Interaction Database: RAP1A
	KEGG: RAP1A
	REACTOME: RAP1A
	ConsensusPathDB
	Pathway Commons: RAP1A
Metabolism	MetaCyc: RAP1A
	HUMANCyc: RAP1A
Regulation	Ensembl's Regulation: ENSG00000116473
	miRBase: chr1 :112,162,404-112,256,101
	TargetScan: NM_001010935
	cisRED: ENSG00000116473
Context	iHOP: RAP1A
	cancer metabolism search in PubMed: RAP1A
	UCL Cancer Institute: RAP1A
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for RAP1A(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

Others
OMIM	179520; gene.
Orphanet
Disease	KEGG Disease: RAP1A
	MedGen: RAP1A (Human Medical Genetics with Condition)
	ClinVar: RAP1A
Phenotype	MGI: RAP1A (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows RAP1A related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
CR997446	RAP1A	1	72	1	112162464	112162535	EIF4A3	71	607	17	78113865	78120850
AA525220	RAP1A	40	124	1	112255650	112255734	RAP1A	112	193	1	112255573	112255654
AI207431	TRAM1	1	216	8	71516081	71516296	RAP1A	209	673	1	112255277	112255741
AA525882	RAP1A	8	92	1	112255650	112255734	RAP1A	80	161	1	112255573	112255654
BF948052	PCDH7	9	264	4	31144315	31144576	RAP1A	255	596	1	112237972	112247049
BF329177	RAP1A	10	128	1	112203562	112203680	SEL1L	114	360	14	81964757	81969115
BP418289	RAP1A	1	28	1	112196355	112196382	RAP1A	22	178	1	112196374	112196530
AK098133	RAP1A	1	519	1	112193133	112193650	EIF4G1	518	2322	3	184045905	184052842

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr1:112240096-112240096	p.E54K	2
chr1:112251778-112251778	p.Y159C	2
chr1:112246984-112246984	p.G115D	2
chr1:112247055-112247055	p.C139G	1
chr1:112234014-112234014	p.S11L	1
chr1:112247110-112247110	p.?	1
chr1:112234037-112234037	p.L19V	1
chr1:112246021-112246021	p.S83A	1
chr1:112234040-112234040	p.?	1
chr1:112246033-112246033	p.Q87K	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1			2								2	1				3	2		2
# mutation	1			2								2	1				3	2		2
nonsynonymous SNV	1			2								2	1				2	2		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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr1:112246984	p.G115D,RAP1A	2
chr1:112234014	p.K5N,RAP1A	1
chr1:112238006	p.S11L,RAP1A	1
chr1:112238020	p.P34Q,RAP1A	1
chr1:112238021	p.S39P,RAP1A	1
chr1:112240080	p.S39F,RAP1A	1
chr1:112240096	p.C48C,RAP1A	1
chr1:112246033	p.E54K,RAP1A	1
chr1:112246040	p.Q87K,RAP1A	1
chr1:112246968	p.T89M,RAP1A	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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