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 RPS6

Basic gene info.	Gene symbol	RPS6
	Gene name	ribosomal protein S6
	Synonyms	S6
	Cytomap	UCSC genome browser: 9p21
	Genomic location	chr9 :19376253-19380235
	Type of gene	protein-coding
	RefGenes	NM_001010.2,
	Ensembl id	ENSG00000137154
	Description	40S ribosomal protein S6phosphoprotein NP33
	Modification date	20141207
dbXrefs	MIM : 180460
	HGNC : HGNC
	Ensembl : ENSG00000137154
	HPRD : 01592
	Vega : OTTHUMG00000019642
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPS6
	BioGPS: 6194
	Gene Expression Atlas: ENSG00000137154
	The Human Protein Atlas: ENSG00000137154
Pathway	NCI Pathway Interaction Database: RPS6
	KEGG: RPS6
	REACTOME: RPS6
	ConsensusPathDB
	Pathway Commons: RPS6
Metabolism	MetaCyc: RPS6
	HUMANCyc: RPS6
Regulation	Ensembl's Regulation: ENSG00000137154
	miRBase: chr9 :19,376,253-19,380,235
	TargetScan: NM_001010
	cisRED: ENSG00000137154
Context	iHOP: RPS6
	cancer metabolism search in PubMed: RPS6
	UCL Cancer Institute: RPS6
Assigned class in ccmGDB	C

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Phenotypic Information for RPS6(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RPS6
	Familial Cancer Database: RPS6

* 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: RPS6
	MedGen: RPS6 (Human Medical Genetics with Condition)
	ClinVar: RPS6
Phenotype	MGI: RPS6 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RPS6

Mutations for RPS6

* 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 RPS6 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
BE257666	RPS6	11	524	9	19376628	19379618	C14orf132	524	621	14	96558852	96558949
CD520454	RPS6	2	190	9	19378437	19378818	MAP2K1	182	216	15	66738791	66738825
AA026363	RPS6	12	241	9	19376253	19376587	POSTN	236	458	13	38137332	38138699
BF843060	RPS6	8	250	9	19376611	19378762	IVL	245	321	1	152884030	152884106
AW973590	RPS6	1	140	9	19376324	19376568	NPAS2	139	462	2	101541622	101554305
BG874971	NUP160	1	237	11	47800453	47800689	RPS6	232	421	9	19378461	19378842
BF514651	RPS6	17	330	9	19376253	19378387	GANAB	329	405	11	62406928	62407163
BF814502	RPS6	7	312	9	19378722	19379594	MALAT1	304	530	11	65266525	65266751
BF814212	MALAT1	220	357	11	65266525	65266662	RPS6	349	560	9	19378815	19379594
BQ378142	RPS6	2	384	9	19378367	19379509	NARS2	371	514	11	78277177	78277320
AA553904	RPS6	6	210	9	19376259	19376568	NPAS2	209	435	2	101541622	101549457
BF815928	RPS6	11	331	9	19378705	19379594	MALAT1	323	571	11	65266525	65266773
BF815926	MALAT1	35	369	11	65266525	65266860	RPS6	361	661	9	19378726	19379594
BG575834	RPS6	1	143	9	19378458	19378792	CASP8	125	828	2	202098783	202105638
T59674	RPS6	1	150	9	19376253	19376507	RPL27	150	432	17	41150472	41152121
AW970974	RPS6	111	480	9	19376905	19377274	RPS6	476	540	9	19376844	19376908
AV697913	RPS6	151	296	9	19376253	19376507	NDST3	287	310	4	118999891	118999914

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

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

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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=21)	Stat. for Synonymous SNVs (# total SNVs=4)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	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
chr9:19376575-19376575	p.R191C	2
chr9:19376543-19376543	p.K201N	1
chr9:19378776-19378776	p.K93N	1
chr9:19376294-19376294	p.K249K	1
chr9:19376553-19376553	p.R198H	1
chr9:19378843-19378843	p.G71D	1
chr9:19376297-19376297	p.Q248H	1
chr9:19376564-19376564	p.L194L	1
chr9:19378869-19378869	p.P62P	1
chr9:19376329-19376329	p.R238*	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	5	2		3								1	2				1	1		6
# mutation	5	2		3								1	2				1	1		6
nonsynonymous SNV	3	2		2								1	1				1	1		6
synonymous SNV	2			1									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
chr9:19376648	p.K249K	1
chr9:19376294	p.P62H	1
chr9:19378419	p.Q248H	1
chr9:19376297	p.A33T	1
chr9:19378482	p.R233I	1
chr9:19376343	p.L24H	1
chr9:19378776	p.R232H	1
chr9:19376346	p.P8L	1
chr9:19378843	p.K230N	1
chr9:19376351	p.M1I	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 RPS6 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 RPS6

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.

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Protein Expression Plot (RPPA)

*RPPA protein expression data were extracted from TCPA (The Cancer Proteome Atlas). Normalized data based on replicated based normalization (RBN) was used to draw following figures.

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


RPL11,RPL12,RPL14,RPL24,RPL27A,RPL29,RPL31, RPL32,RPL34,RPL35A,RPL37,RPL37A,RPL5,RPL6, RPL7A,RPS18,RPS19,RPS4X,RPS6,RPS7,RPS8	GNB2L1,RPL10,RPL10A,RPL12,RPL14,RPL24,RPL32, RPL35A,RPL37,RPL4,RPL5,RPL6,RPLP0,RPS12, RPS14,RPS18,RPS3A,RPS4X,RPS6,RPS7,RPS8

EEF1B2,RPL10A,RPL15,RPL31,RPL32,RPL35,RPL35A, RPL36,RPL5,RPL7A,RPS10,RPS11,RPS13,RPS14, RPS15A,RPS18,RPS23,RPS3,RPS6,RPS7,RPS8	TMEM261,EEF1B2,MED28,RPL24,RPL27A,RPL35,RPL41, RPL5,RPS10,RPS11,RPS14,RPS18,RPS3,RPS3A, RPS5,RPS6,RPS7,RPS8,RPSAP58,SNRPD2,TMEM14B

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 RPS6

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00877	ribosomal protein S6	approved; investigational	Sirolimus

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Cross referenced IDs for RPS6

* 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