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 RPL23

Basic gene info.	Gene symbol	RPL23
	Gene name	ribosomal protein L23
	Synonyms	L23\|rpL17
	Cytomap	UCSC genome browser: 17q
	Genomic location	chr17 :37006320-37010053
	Type of gene	protein-coding
	RefGenes	NM_000978.3,
	Ensembl id	ENSG00000125691
	Description	60S ribosomal protein L1760S ribosomal protein L23ribosomal protein L17
	Modification date	20141207
dbXrefs	MIM : 603662
	HGNC : HGNC
	HPRD : 04716
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPL23
	BioGPS: 9349
	Gene Expression Atlas: ENSG00000125691
	The Human Protein Atlas: ENSG00000125691
Pathway	NCI Pathway Interaction Database: RPL23
	KEGG: RPL23
	REACTOME: RPL23
	ConsensusPathDB
	Pathway Commons: RPL23
Metabolism	MetaCyc: RPL23
	HUMANCyc: RPL23
Regulation	Ensembl's Regulation: ENSG00000125691
	miRBase: chr17 :37,006,320-37,010,053
	TargetScan: NM_000978
	cisRED: ENSG00000125691
Context	iHOP: RPL23
	cancer metabolism search in PubMed: RPL23
	UCL Cancer Institute: RPL23
Assigned class in ccmGDB	C

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Phenotypic Information for RPL23(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RPL23
	Familial Cancer Database: RPL23

* 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: RPL23
	MedGen: RPL23 (Human Medical Genetics with Condition)
	ClinVar: RPL23
Phenotype	MGI: RPL23 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RPL23

Mutations for RPL23

* 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 RPL23 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
AI968908	RPL23	1	149	17	37008942	37009971	DFFA	146	259	1	10521426	10521539
DB573606	PRR14	1	171	16	30667374	30667544	RPL23	162	464	17	37006342	37008919
BG878350	RPL23	77	292	17	37008857	37009360	JARID2	274	293	6	15498498	15498517
AW594130	RPL23	1	152	17	37008942	37009974	DFFA	149	262	1	10521426	10521539
DW440511	GAPDH	18	187	12	6643683	6646535	RPL23	185	386	17	37008897	37009979
DR002474	RPL23	32	526	17	37006334	37009988	ARL8B	520	539	3	5220038	5220057
BE265135	RPL23	1	135	17	37006343	37006621	MRPL10	135	657	17	45904007	45908870
BQ311440	JARID2	151	172	6	15498498	15498519	RPL23	171	339	17	37006414	37006729
CB138512	SERPINA1	21	221	14	94844710	94844909	RPL23	207	338	17	37006649	37008908
AI962592	RPL23	1	152	17	37008942	37009974	DFFA	149	262	1	10521426	10521539
BU677197	ARHGEF3	1	27	3	56925201	56925404	RPL23	18	269	17	37006331	37006729
AA045738	PALLD	1	192	4	169849369	169849560	RPL23	185	393	17	37006342	37006699
T90988	RPL23	1	139	17	37006366	37006650	CENPF	125	373	1	214819188	214819433
BY999398	RPL23	1	320	17	37006358	37008951	MED30	301	320	8	118545351	118545370
CB134886	SERPINA1	21	220	14	94844710	94844909	RPL23	206	488	17	37006350	37008908
CB147374	SERPINA1	21	220	14	94844710	94844909	RPL23	206	458	17	37006381	37008908
DA438824	RPL23	1	113	17	37009278	37009982	CD164	108	598	6	109689728	109690218
CB147414	SERPINA1	21	220	14	94844710	94844909	RPL23	206	488	17	37006350	37008908
CB137683	SERPINA1	21	220	14	94844710	94844909	RPL23	206	488	17	37006350	37008908
DB216263	RPL23	1	100	17	37009298	37009989	C10orf137	101	500	10	127408279	127409966
CB135233	SERPINA1	21	220	14	94844710	94844909	RPL23	206	488	17	37006350	37008908

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=8)	Stat. for Synonymous SNVs (# total SNVs=2)

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
chr17:37006676-37006676	p.G93G	1
chr17:37008870-37008870	p.E71D	1
chr17:37008911-37008911	p.G58C	1
chr17:37009284-37009284	p.D30N	1
chr17:37009289-37009289	p.C28F	1
chr17:37006411-37006411	p.A133T	1
chr17:37009327-37009327	p.R15R	1
chr17:37006457-37006457	p.I117I	1
chr17:37009328-37009328	p.R15Q	1
chr17:37006464-37006464	p.S115F	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												1	3
# mutation				1			2												1	3
nonsynonymous SNV							1													2
synonymous SNV				1			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
chr17:37009327	p.I117I	1
chr17:37009953	p.I105V	1
chr17:37006457	p.G93G	1
chr17:37006642	p.E71D	1
chr17:37006676	p.G58C	1
chr17:37008870	p.R48R	1
chr17:37008911	p.R15R	1
chr17:37008939	p.R4P	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 RPL23 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 RPL23

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 RPL23

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 L23	experimental	Alpha-Hydroxy-Beta-Phenyl-Propionic Acid
DB07374	ribosomal protein L23	experimental	ANISOMYCIN
DB08437	ribosomal protein L23	experimental	PUROMYCIN

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Cross referenced IDs for RPL23

* 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