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 RPL23A

Basic gene info.	Gene symbol	RPL23A
	Gene name	ribosomal protein L23a
	Synonyms	L23A\|MDA20
	Cytomap	UCSC genome browser: 17q11.2
	Genomic location	chr17 :27046999-27051374
	Type of gene	protein-coding
	RefGenes	NM_000984.5,
	Ensembl id	ENSG00000198242
	Description	60S ribosomal protein L23amelanoma differentiation-associated gene 20
	Modification date	20141207
dbXrefs	MIM : 602326
	HGNC : HGNC
	HPRD : 15998
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPL23A
	BioGPS: 6147
	Gene Expression Atlas: ENSG00000198242
	The Human Protein Atlas: ENSG00000198242
Pathway	NCI Pathway Interaction Database: RPL23A
	KEGG: RPL23A
	REACTOME: RPL23A
	ConsensusPathDB
	Pathway Commons: RPL23A
Metabolism	MetaCyc: RPL23A
	HUMANCyc: RPL23A
Regulation	Ensembl's Regulation: ENSG00000198242
	miRBase: chr17 :27,046,999-27,051,374
	TargetScan: NM_000984
	cisRED: ENSG00000198242
Context	iHOP: RPL23A
	cancer metabolism search in PubMed: RPL23A
	UCL Cancer Institute: RPL23A
Assigned class in ccmGDB	C

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Phenotypic Information for RPL23A(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RPL23A
	Familial Cancer Database: RPL23A

* 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: RPL23A
	MedGen: RPL23A (Human Medical Genetics with Condition)
	ClinVar: RPL23A
Phenotype	MGI: RPL23A (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RPL23A

Mutations for RPL23A

* 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 RPL23A 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
DB117326	RPL23A	1	44	17	27047590	27047633	UBC	45	639	12	125397790	125399196
BP259075	CMYA5	1	460	5	79033762	79034220	RPL23A	452	574	17	27047863	27049817
BG623888	RPL23A	1	54	17	27050449	27050502	NAA15	46	701	4	140278552	140283091
BQ943640	CCDC43	86	356	17	42756377	42761280	RPL23A	357	743	17	27047024	27049913
AW090311	RPL23A	15	61	17	27050908	27050954	SPEF2	53	486	5	35651430	35651862
BC007583	TRBV20-1	43	985	16	2012062	2014652	RPL23A	985	1487	17	27047723	27050954

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=9)	Stat. for Synonymous SNVs (# total SNVs=4)

Stat. for Deletions (# total SNVs=2)	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
chr17:27047808-27047810	p.K39delK	2
chr17:27047880-27047880	p.P61A	1
chr17:27049755-27049755	p.A75D	1
chr17:27049769-27049770	p.P80L	1
chr17:27047044-27047044	p.K7K	1
chr17:27050593-27050593	p.D131H	1
chr17:27047724-27047724	p.?	1
chr17:27050601-27050601	p.E133D	1
chr17:27050606-27050606	p.K135R	1
chr17:27047813-27047813	p.K38K	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			2								3	1	1						3
# mutation	1			2								3	1	1						3
nonsynonymous SNV	1			1								2		1						3
synonymous SNV				1								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
chr17:27050613	p.K38K	1
chr17:27050632	p.I40T	1
chr17:27050643	p.R41C	1
chr17:27047813	p.S43L	1
chr17:27047818	p.R47W	1
chr17:27047820	p.P49P	1
chr17:27047827	p.A75D	1
chr17:27047838	p.E133D	1
chr17:27047846	p.Y137Y	1
chr17:27049755	p.Y144D	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 RPL23A 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 RPL23A

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


EEF1G,ERAL1,FLOT2,IFT20,POLDIP2,RAB34,RPL13, RPL18A,RPL23A,RPL32,RPL36,RPL41,RPL6,RPLP0, RPS11,RPS5,SDF2,TLCD1,TMEM199,TRAF4,UBA52	BTF3,CCT4,EEF1A1,RPL10,RPL10A,RPL14,RPL22, RPL23A,RPL24,RPL30,RPL31,RPL32,RPL34,RPL35A, RPL37,RPL41,RPL6,RPS15A,RPS27A,RPS4X,RPS7

EEF1G,EIF1,NME2,RPL18A,RPL23,RPL23A,RPL27, RPL28,RPL38,RPL39,RPL41,RPL7,RPLP0,RPS13, RPS16,RPS2,RPS29,RPS3,RPS9,TMEM101,UBA52	EEF1A1,EEF1G,EIF3H,GNB2L1,RPL10,RPL13,RPL19, RPL23A,RPL30,RPL32,RPL3,RPL36,RPL37,RPL37A, RPL38,RPLP2,RPS12,RPS19,RPS23,RPS25,UBA52

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 RPL23A

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 L23a	experimental	Alpha-Hydroxy-Beta-Phenyl-Propionic Acid
DB07374	ribosomal protein L23a	experimental	ANISOMYCIN
DB08437	ribosomal protein L23a	experimental	PUROMYCIN

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Cross referenced IDs for RPL23A

* 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