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 RAP1B

Basic gene info.	Gene symbol	RAP1B
	Gene name	RAP1B, member of RAS oncogene family
	Synonyms	K-REV\|RAL1B
	Cytomap	UCSC genome browser: 12q14
	Genomic location	chr12 :69004618-69054385
	Type of gene	protein-coding
	RefGenes	NM_001010942.2, NM_001251917.1,NM_001251918.1,NM_001251921.1,NM_001251922.1, NM_015646.5,
	Ensembl id	ENSG00000127314
	Description	GTP-binding protein smg p21BRAS-related protein RAP1BRas family small GTP binding protein RAP1Bras-related protein Rap-1bsmall GTP binding protein
	Modification date	20141207
dbXrefs	MIM : 179530
	HGNC : HGNC
	Ensembl : ENSG00000127314
	HPRD : 01546
	Vega : OTTHUMG00000133660
Protein	UniProt: P61224 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RAP1B
	BioGPS: 5908
	Gene Expression Atlas: ENSG00000127314
	The Human Protein Atlas: ENSG00000127314
Pathway	NCI Pathway Interaction Database: RAP1B
	KEGG: RAP1B
	REACTOME: RAP1B
	ConsensusPathDB
	Pathway Commons: RAP1B
Metabolism	MetaCyc: RAP1B
	HUMANCyc: RAP1B
Regulation	Ensembl's Regulation: ENSG00000127314
	miRBase: chr12 :69,004,618-69,054,385
	TargetScan: NM_001010942
	cisRED: ENSG00000127314
Context	iHOP: RAP1B
	cancer metabolism search in PubMed: RAP1B
	UCL Cancer Institute: RAP1B
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for RAP1B(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

Others
OMIM	179530; gene. 179530; gene.
Orphanet
Disease	KEGG Disease: RAP1B
	MedGen: RAP1B (Human Medical Genetics with Condition)
	ClinVar: RAP1B
Phenotype	MGI: RAP1B (International Mouse Phenotyping Consortium)
Phenotype	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.

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 RAP1B 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
CB243131	TLCD2	7	98	17	1608327	1608418	RAP1B	94	165	12	69020556	69020646
CA428502	RAP1B	1	58	12	69020573	69020632	HUWE1	55	180	X	53565825	53565950
BC057387	LSM14B	1	2629	20	60697517	60704636	RAP1B	2621	2685	12	69020555	69020638
BF327763	RAP1B	18	101	12	69032118	69032201	TUBGCP3	99	181	13	113193332	113193414

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	ns	ovary	pancre	prost	skin	stoma	thyro	urina
Total # sample	2	8							3		1			2	1		1
GAIN (# sample)	2	8							3		1			2	1		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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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=4

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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=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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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
chr12:69042539-69042539	p.G12E	3
chr12:69042508-69042508	p.R2C	1
chr12:69044195-69044195	p.Q25E	1
chr12:69047944-69047944	p.A79V	1
chr12:69042512-69042512	p.E3G	1
chr12:69044198-69044198	p.G26*	1
chr12:69048013-69048013	p.R102Q	1
chr12:69042518-69042518	p.K5R	1
chr12:69044218-69044218	p.Y32Y	1
chr12:69050104-69050104	p.G115C	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=3

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	2			2			1		3		1	3	1					6		4
# mutation	2			2			1		3		1	3	1					6		4
nonsynonymous SNV	2			2			1		2		1	2	1					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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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
chr12:69042539	p.G12E,RAP1B	3
chr12:69042508	p.A37V,RAP1B	1
chr12:69044231	p.R60Q,RAP1B	1
chr12:69042512	p.R2C,RAP1B	1
chr12:69045809	p.G73C,RAP1B	1
chr12:69042518	p.E3G,RAP1B	1
chr12:69047922	p.R121R,RAP1B	1
chr12:69047944	p.K5R,RAP1B	1
chr12:69042542	p.G131V,RAP1B	1
chr12:69048013	p.R134H,RAP1B	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 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

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


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

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 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