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 RPL13A

Basic gene info.	Gene symbol	RPL13A
	Gene name	ribosomal protein L13a
	Synonyms	L13A\|TSTA1
	Cytomap	UCSC genome browser: 19q13.3
	Genomic location	chr19 :49990864-49995564
	Type of gene	protein-coding
	RefGenes	NM_001270491.1, NM_012423.3,NR_073024.1,
	Ensembl id	ENSG00000142541
	Description	23 kDa highly basic protein60S ribosomal protein L13atissue specific transplantation antigen 1
	Modification date	20141207
dbXrefs	HGNC : HGNC
	Ensembl : ENSG00000142541
	HPRD : 11775
	Vega : OTTHUMG00000134289
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPL13A
	BioGPS: 23521
	Gene Expression Atlas: ENSG00000142541
	The Human Protein Atlas: ENSG00000142541
Pathway	NCI Pathway Interaction Database: RPL13A
	KEGG: RPL13A
	REACTOME: RPL13A
	ConsensusPathDB
	Pathway Commons: RPL13A
Metabolism	MetaCyc: RPL13A
	HUMANCyc: RPL13A
Regulation	Ensembl's Regulation: ENSG00000142541
	miRBase: chr19 :49,990,864-49,995,564
	TargetScan: NM_001270491
	cisRED: ENSG00000142541
Context	iHOP: RPL13A
	cancer metabolism search in PubMed: RPL13A
	UCL Cancer Institute: RPL13A
Assigned class in ccmGDB	C

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Phenotypic Information for RPL13A(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RPL13A
	Familial Cancer Database: RPL13A

* 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: RPL13A
	MedGen: RPL13A (Human Medical Genetics with Condition)
	ClinVar: RPL13A
Phenotype	MGI: RPL13A (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RPL13A

Mutations for RPL13A

* 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 RPL13A 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
EC557264	RPL13A	1	68	19	49993738	49993805	GTF2IP1	62	128	7	74601404	74601470
BP333446	RPL13A	1	251	19	49995135	49995386	KAZN	243	262	1	15306034	15306053
BG255829	BHLHE40	1	348	3	5024668	5025014	RPL13A	343	638	19	49993758	49994768
AX747058	ANKRD52	1	2297	12	56636333	56645863	RPL13A	2294	2707	19	49993801	49995097
BM677070	RPL13A	12	150	19	49995427	49995565	ACTG1	144	683	17	79478723	79479353
BM723492	RPL13A	1	101	19	49993117	49993526	ARL6IP5	101	243	3	69153989	69154131
X06537	RPL13A	1	163	19	49995147	49995310	LCAT	151	1447	16	67973786	67977957
BU683473	RPL13A	16	69	19	49995512	49995565	FZD7	63	684	2	202902537	202903164
BM838228	RPL13A	1	94	19	49487554	49492308	ACTG1	94	601	17	81509971	81512890

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=8)	Stat. for Synonymous SNVs (# total SNVs=5)

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
chr19:49995055-49995055	p.H199Y	2
chr19:49993823-49993823	p.R82R	2
chr19:49994304-49994304	p.R117Q	2
chr19:49993748-49993748	p.F57F	1
chr19:49994339-49994339	p.L129L	1
chr19:49993749-49993749	p.L58F	1
chr19:49994349-49994349	p.T132I	1
chr19:49993753-49993753	p.R59L	1
chr19:49994985-49994985	p.?	1
chr19:49993146-49993146	p.L19L	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		3	2		1		1					2					4	2		4
# mutation		3	2		1		1					2					4	2		5
nonsynonymous SNV		3	2		1		1					1					2	2		1
synonymous SNV												1					2			4

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
chr19:49993733	p.L58F	1
chr19:49994339	p.R59L	1
chr19:49993743	p.R61W	1
chr19:49995048	p.N4K,RPL13A	1
chr19:49993749	p.P15S,RPL13A	1
chr19:49995067	p.P50L,RPL13A	1
chr19:49993753	p.Y51Y,RPL13A	1
chr19:49993146	p.L19L	1
chr19:49993758	p.R56W,RPL13A	1
chr19:49993179	p.G30S	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 RPL13A 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 RPL13A

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


GLTSCR2,RPL10,RPL10A,RPL11,RPL13A,RPL13AP20,RPL13AP3, RPL18,RPL28,RPL29,RPL3,RPL37A,RPL7A,RPLP0, RPS11,RPS14,RPS19,RPS23,RPS5,RPS8,RPS9	FBL,GNB2L1,RPL10,RPL10A,RPL13,RPL13A,RPL18, RPL18A,RPL19,RPL29,RPL3,RPL36,RPL7A,RPL8, RPS14,RPS19,RPS21,RPS2,RPS3,RPS5,RPS8

LRRC75A-AS1,RPL10A,RPL12,RPL13A,RPL13AP3,RPL18,RPL28, RPL3,RPL41,RPL7A,RPLP0,RPS11,RPS15,RPS16, RPS19,RPS3,RPS5,RPS8,RPS9,SNRPD2,ZNF581	ATP5G2,RPL10,RPL13A,RPL14,RPL18,RPL18A,RPL19, RPL29,RPL32,RPL3,RPL36,RPL7A,RPL8,RPLP0, RPLP1,RPS11,RPS12,RPS3,RPS5,RPS8,RPS9

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 RPL13A

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
DB02494	ribosomal protein L13a	experimental	Alpha-Hydroxy-Beta-Phenyl-Propionic Acid
DB07374	ribosomal protein L13a	experimental	ANISOMYCIN
DB08437	ribosomal protein L13a	experimental	PUROMYCIN

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Cross referenced IDs for RPL13A

* 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