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 RPS13

Basic gene info.	Gene symbol	RPS13
	Gene name	ribosomal protein S13
	Synonyms	S13
	Cytomap	UCSC genome browser: 11p15
	Genomic location	chr11 :17095938-17099220
	Type of gene	protein-coding
	RefGenes	NM_001017.2,
	Ensembl id	ENSG00000110700
	Description	40S ribosomal protein S13
	Modification date	20141207
dbXrefs	MIM : 180476
	HGNC : HGNC
	Ensembl : ENSG00000110700
	HPRD : 01604
	Vega : OTTHUMG00000165988
Protein	UniProt: P62277 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPS13
	BioGPS: 6207
	Gene Expression Atlas: ENSG00000110700
	The Human Protein Atlas: ENSG00000110700
Pathway	NCI Pathway Interaction Database: RPS13
	KEGG: RPS13
	REACTOME: RPS13
	ConsensusPathDB
	Pathway Commons: RPS13
Metabolism	MetaCyc: RPS13
	HUMANCyc: RPS13
Regulation	Ensembl's Regulation: ENSG00000110700
	miRBase: chr11 :17,095,938-17,099,220
	TargetScan: NM_001017
	cisRED: ENSG00000110700
Context	iHOP: RPS13
	cancer metabolism search in PubMed: RPS13
	UCL Cancer Institute: RPS13
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for RPS13(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RPS13
	Familial Cancer Database: RPS13

* 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	180476; gene.
Orphanet
Disease	KEGG Disease: RPS13
	MedGen: RPS13 (Human Medical Genetics with Condition)
	ClinVar: RPS13
Phenotype	MGI: RPS13 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RPS13

Mutations for RPS13

* 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 RPS13 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
BQ324806	RPS13	12	380	11	17096659	17099010	HDGF	372	554	1	156713960	156714142
BU935289	SNRPD1	4	404	18	19192307	19209056	RPS13	403	576	11	17095944	17096746
BG110883	ATXN7L3B	1	469	12	74932804	74933276	RPS13	461	768	11	17096656	17098766
BU195584	RPS13	11	440	11	17096649	17099201	RPS13	438	788	11	17096644	17098793

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=11)	Stat. for Synonymous SNVs (# total SNVs=3)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=2)
There's no deleted 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
chr11:17097027-17097027	p.R99G	3
chr11:17096743-17096743	p.D108V	3
chr11:17097026-17097026	p.R99Q	1
chr11:17099170-17099170	p.P7S	1
chr11:17099177-17099177	p.M4I	1
chr11:17097072-17097072	p.L84F	1
chr11:17099182-17099182	p.R3C	1
chr11:17098743-17098743	p.A41A	1
chr11:17098745-17098745	p.A41T	1
chr11:17098755-17098755	p.I37M	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			3			2		1								1	1		1
# mutation	1			3			2		1								1	1		1
nonsynonymous SNV	1			2			2		1								1	1		1
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
chr11:17097026	p.K70T	1
chr11:17097113	p.A41A	1
chr11:17098743	p.A41T	1
chr11:17098745	p.I37M	1
chr11:17098755	p.L28V	1
chr11:17098784	p.R19G	1
chr11:17098993	p.M4I	1
chr11:17099177	p.R3C	1
chr11:17099182	p.A151P	1
chr11:17095985	p.R99Q	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 RPS13 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 RPS13

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


EEF1B2,EIF3F,RPL10A,RPL11,RPL14,RPL17,RPL27A, RPL31,RPL34,RPL37A,RPLP0,RPLP2,RPS13,RPS14, RPS18,RPS23,RPS25,RPS27A,RPS29,RPS8,RPSAP58	BTF3,C18orf21,C8orf59,COMMD6,EIF3H,EIF3M,HINT1, RPL15,RPL22,RPL30,RPL32,RPL34,RPL35A,RPL38, RPL41,RPS13,RPS15A,RPS29,RPS3A,TIMM9,UXT

EEF1B2,RPL10A,RPL14,RPL29,RPL32,RPL35A,RPL36, RPL37A,RPL38,RPLP2,RPS10,RPS11,RPS13,RPS14, RPS15A,RPS18,RPS23,RPS25,RPS3,RPS6,RPS8	EEF1A1,EEF1B2,FAU,PFDN5,RPL15,RPL24,RPL27A, RPL32,RPL35,RPL35A,RPL38,RPL41,RPL5,RPL7A, RPS10,RPS11,RPS13,RPS3A,RPS5,RPS6,SNRPD2

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 RPS13

There's no related Drug.

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Cross referenced IDs for RPS13

* 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