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 RPS5

Basic gene info.	Gene symbol	RPS5
	Gene name	ribosomal protein S5
	Synonyms	S5
	Cytomap	UCSC genome browser: 19q13.4
	Genomic location	chr19 :58898635-58906171
	Type of gene	protein-coding
	RefGenes	NM_001009.3,
	Ensembl id	ENSG00000083845
	Description	40S ribosomal protein S5
	Modification date	20141207
dbXrefs	MIM : 603630
	HGNC : HGNC
	Ensembl : ENSG00000083845
	HPRD : 04695
	Vega : OTTHUMG00000183530
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPS5
	BioGPS: 6193
	Gene Expression Atlas: ENSG00000083845
	The Human Protein Atlas: ENSG00000083845
Pathway	NCI Pathway Interaction Database: RPS5
	KEGG: RPS5
	REACTOME: RPS5
	ConsensusPathDB
	Pathway Commons: RPS5
Metabolism	MetaCyc: RPS5
	HUMANCyc: RPS5
Regulation	Ensembl's Regulation: ENSG00000083845
	miRBase: chr19 :58,898,635-58,906,171
	TargetScan: NM_001009
	cisRED: ENSG00000083845
Context	iHOP: RPS5
	cancer metabolism search in PubMed: RPS5
	UCL Cancer Institute: RPS5
Assigned class in ccmGDB	C

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Phenotypic Information for RPS5(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RPS5
	Familial Cancer Database: RPS5

* 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_METABOLISM_OF_PROTEINS REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM
Orphanet
Disease	KEGG Disease: RPS5
	MedGen: RPS5 (Human Medical Genetics with Condition)
	ClinVar: RPS5
Phenotype	MGI: RPS5 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RPS5

Mutations for RPS5

* 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

- Statistics for Tissue and Mutation type

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- For Inter-chromosomal Variations

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- For Intra-chromosomal Variations

There's no intra-chromosomal structural variation.

Sample

Symbol_a

Chr_a

Start_a

End_a

Symbol_b

Chr_b

Start_b

End_b

cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows RPS5 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
BG929094	SPIN3	65	417	X	57017834	57018186	RPS5	411	590	19	58905861	58906126
CF128579	CD63	1	675	12	56119614	56122766	RPS5	675	815	19	58904396	58904536
BU175700	MRPS21	1	381	1	150266791	150280782	RPS5	381	604	19	58904724	58905959
BQ432456	CTDSP1	1	155	2	219264611	219264765	RPS5	156	617	19	58904350	58906080
U50079	RPS5	1	96	19	58898660	58899554	HDAC1	97	1611	1	32757757	32798767
BQ227834	ACTG1	5	289	17	79477001	79477287	RPS5	290	655	19	58898661	58904552

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=12)	Stat. for Synonymous SNVs (# total SNVs=11)

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
chr19:58904820-58904820	p.A138V	2
chr19:58904396-58904396	p.G54G	2
chr19:58904798-58904798	p.A131T	1
chr19:58906110-58906110	p.N203S	1
chr19:58904471-58904471	p.H79H	1
chr19:58904801-58904801	p.G132R	1
chr19:58899511-58899511	p.E3K	1
chr19:58904472-58904472	p.G80S	1
chr19:58904809-58904809	p.V134V	1
chr19:58899536-58899536	p.V11G	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		4	1	3	1		1					2	1				3	4		3
# mutation		4	1	3	1		1					2	1				3	4		3
nonsynonymous SNV		4		2	1		1										1	3
synonymous SNV			1	1								2	1				2	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
chr19:58904809	p.V134V	2
chr19:58906108	p.A138V	1
chr19:58904732	p.C172C	1
chr19:58906110	p.E3Q	1
chr19:58899511	p.A174S	1
chr19:58904744	p.D16D	1
chr19:58899552	p.S185S	1
chr19:58904783	p.F20L	1
chr19:58899562	p.S187F	1
chr19:58899606	p.S34S	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 RPS5 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 RPS5

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


C19orf48,RPL10,RPL10A,RPL13A,RPL13AP20,RPL18,RPL28, RPL36,RPL37A,RPLP0,RPS10,RPS11,RPS14,RPS19, RPS5,RPS8,RPS9,RPSA,RPSAP58,TRIM28,ZNF581	EEF1G,GNB2L1,RPL10,RPL10A,RPL12,RPL13A,RPL14, RPL18,RPL18A,RPL19,RPL3,RPL7A,RPLP0,RPS14, RPS19,RPS2,RPS3,RPS5,RPS6,RPS8,RPSAP58

EEF1B2,LRRC75A-AS1,RPL10A,RPL13A,RPL18,RPL28,RPL35, RPLP0,RPS10,RPS11,RPS14,RPS16,RPS19,RPS29, RPS3,RPS3A,RPS5,RPS9,RPSAP58,SNRPD2,ZNF581	C12orf57,EEF1B2,RPL10A,RPL15,RPL24,RPL27A,RPL29, RPL32,RPL35,RPL41,RPL5,RPL7A,RPS10,RPS11, RPS14,RPS3,RPS3A,RPS5,RPS6,RPS8,RPSAP58

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 RPS5

There's no related Drug.

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Cross referenced IDs for RPS5

* 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