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 RPS8

Basic gene info.	Gene symbol	RPS8
	Gene name	ribosomal protein S8
	Synonyms	S8
	Cytomap	UCSC genome browser: 1p34.1-p32
	Genomic location	chr1 :45241245-45244412
	Type of gene	protein-coding
	RefGenes	NM_001012.1,
	Ensembl id	ENSG00000142937
	Description	40S ribosomal protein S8OK/SW-cl.83
	Modification date	20141207
dbXrefs	MIM : 600357
	HGNC : HGNC
	Ensembl : ENSG00000142937
	HPRD : 15969
	Vega : OTTHUMG00000008494
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPS8
	BioGPS: 6202
	Gene Expression Atlas: ENSG00000142937
	The Human Protein Atlas: ENSG00000142937
Pathway	NCI Pathway Interaction Database: RPS8
	KEGG: RPS8
	REACTOME: RPS8
	ConsensusPathDB
	Pathway Commons: RPS8
Metabolism	MetaCyc: RPS8
	HUMANCyc: RPS8
Regulation	Ensembl's Regulation: ENSG00000142937
	miRBase: chr1 :45,241,245-45,244,412
	TargetScan: NM_001012
	cisRED: ENSG00000142937
Context	iHOP: RPS8
	cancer metabolism search in PubMed: RPS8
	UCL Cancer Institute: RPS8
Assigned class in ccmGDB	C

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Phenotypic Information for RPS8(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RPS8
	Familial Cancer Database: RPS8

* 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: RPS8
	MedGen: RPS8 (Human Medical Genetics with Condition)
	ClinVar: RPS8
Phenotype	MGI: RPS8 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RPS8

Mutations for RPS8

* 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 RPS8 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
DA657610	RPS8	1	63	1	45244065	45244127	AKT2	64	574	19	40743955	40761110
BG565964	RPS8	1	70	1	45241536	45241605	USP47	64	729	11	11970041	11977607
AK129640	GOLGA2	1	1916	9	131023519	131029481	RPS8	1913	2138	1	45243738	45244409
BM682967	RPS8	17	225	1	45243774	45244427	MAP3K7	226	706	6	91246054	91252594
BF920614	LRRC4C	17	166	11	41080988	41081143	RPS8	162	283	1	45243417	45243748
AW948714	RPS8	10	103	1	45241782	45242410	NISCH	99	382	3	52526529	52526812
BQ082553	DDA1	1	323	19	17431598	17431920	RPS8	320	446	1	45242583	45242709

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=12)	Stat. for Synonymous SNVs (# total SNVs=7)

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
chr1:45244310-45244310	p.E194Q	2
chr1:45243328-45243328	p.A85G	1
chr1:45243749-45243749	p.N155N	1
chr1:45241776-45241776	p.R25R	1
chr1:45243365-45243365	p.V97V	1
chr1:45243758-45243758	p.I158I	1
chr1:45241793-45241793	p.R31L	1
chr1:45243431-45243431	p.L119L	1
chr1:45243760-45243760	p.S159N	1
chr1:45242351-45242352	p.R41fs*12	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=1

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			1			1						2	2			1	2		3
# mutation	1			1			1						3	2			1	2		3
nonsynonymous SNV													2				1			2
synonymous SNV	1			1			1						1	2				2		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
chr1:45243773	p.R49L	1
chr1:45242381	p.K53K	1
chr1:45244276	p.R74C	1
chr1:45242394	p.P120P	1
chr1:45243294	p.L121L	1
chr1:45243434	p.G122G	1
chr1:45243437	p.R123C	1
chr1:45243440	p.P131S	1
chr1:45243441	p.R141Q	1
chr1:45243675	p.N155N	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 RPS8 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 RPS8

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


RPL10,RPL11,RPL12,RPL18,RPL24,RPL27A,RPL31, RPL32,RPL36,RPL37,RPL37A,RPL5,RPL7A,RPLP0, RPLP2,RPS10,RPS18,RPS19,RPS2,RPS8,RPS9	FBL,GNB2L1,RPL10,RPL10A,RPL12,RPL13,RPL13A, RPL14,RPL18,RPL19,RPL24,RPL27A,RPL36,RPL5, RPL7A,RPS11,RPS14,RPS2,RPS3,RPS6,RPS8

RPL10A,RPL12,RPL24,RPL29,RPL32,RPL35,RPL36, RPL5,RPL7A,RPLP0,RPS10,RPS13,RPS14,RPS16, RPS18,RPS29,RPS3,RPS6,RPS7,RPS8,RPS9	DPH5,EEF1B2,RPL10A,RPL15,RPL24,RPL27A,RPL32, RPL5,RPL7A,RPLP0,RPS10,RPS11,RPS14,RPS18, RPS3,RPS3A,RPS5,RPS6,RPS7,RPS8,RPSA

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 RPS8

There's no related Drug.

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Cross referenced IDs for RPS8

* 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