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 RPL3

Basic gene info.	Gene symbol	RPL3
	Gene name	ribosomal protein L3
	Synonyms	ASC-1\|L3\|TARBP-B
	Cytomap	UCSC genome browser: 22q13
	Genomic location	chr22 :39708886-39715670
	Type of gene	protein-coding
	RefGenes	NM_000967.3, NM_001033853.1,
	Ensembl id	ENSG00000100316
	Description	60S ribosomal protein L3HIV-1 TAR RNA-binding protein Bhypothetical protein
	Modification date	20141207
dbXrefs	MIM : 604163
	HGNC : HGNC
	Ensembl : ENSG00000100316
	HPRD : 16042
	Vega : OTTHUMG00000151079
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPL3
	BioGPS: 6122
	Gene Expression Atlas: ENSG00000100316
	The Human Protein Atlas: ENSG00000100316
Pathway	NCI Pathway Interaction Database: RPL3
	KEGG: RPL3
	REACTOME: RPL3
	ConsensusPathDB
	Pathway Commons: RPL3
Metabolism	MetaCyc: RPL3
	HUMANCyc: RPL3
Regulation	Ensembl's Regulation: ENSG00000100316
	miRBase: chr22 :39,708,886-39,715,670
	TargetScan: NM_000967
	cisRED: ENSG00000100316
Context	iHOP: RPL3
	cancer metabolism search in PubMed: RPL3
	UCL Cancer Institute: RPL3
Assigned class in ccmGDB	C

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Phenotypic Information for RPL3(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RPL3
	Familial Cancer Database: RPL3

* 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: RPL3
	MedGen: RPL3 (Human Medical Genetics with Condition)
	ClinVar: RPL3
Phenotype	MGI: RPL3 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RPL3

Mutations for RPL3

* 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

- Statistics for Tissue and Mutation type

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- For Inter-chromosomal Variations

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- For Intra-chromosomal Variations

There's no intra-chromosomal structural variation.

Sample

Symbol_a

Chr_a

Start_a

End_a

Symbol_b

Chr_b

Start_b

End_b

cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows RPL3 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
CN268128	EMILIN1	1	145	2	27301589	27301733	RPL3	141	193	22	39708889	39708941
BQ349966	RPL3	10	328	22	39713539	39715630	RPL3	323	592	22	39710198	39711466
BQ923637	HLA-B	1	48	6	2581523	2581571	RPL3	45	813	22	39710699	39714528
CD699756	LPAR5	42	210	12	6730603	6745126	RPL3	201	606	22	39711434	39713608
AL702234	SEPT11	1	54	4	77949830	77949883	RPL3	48	163	22	39708894	39709215
CV360980	MICB	22	334	6	2594912	2596137	RPL3	331	584	22	39710691	39711466
BP429026	GPX1	7	292	3	49394925	49395489	RPL3	291	388	22	39709703	39710177
BG505035	FLT3LG	2	522	19	49990865	49994778	RPL3	521	637	22	39708915	39709232
BM972994	PPAPDC1B	17	545	8	38124500	38125533	RPL3	539	689	22	39713598	39714519
AA242792	RPL3	1	154	22	39711373	39711526	SOX8	154	490	16	1036443	1036779
CD368190	RPL38	17	208	17	72205334	72206019	RPL3	203	697	22	39710181	39712824
CX786698	RPL3	1	495	22	39711429	39714462	BCL2L2-PABPN1	491	616	14	23795153	23795279
AW999090	NGLY1	15	283	3	25773848	25775506	RPL3	269	539	22	39713058	39713328
BF360749	RPL3	61	213	22	39710691	39710841	STX11	202	222	6	144483951	144483971

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=19)	Stat. for Synonymous SNVs (# total SNVs=10)

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
chr22:39714490-39714490	p.P37P	2
chr22:39713525-39713525	p.F102F	2
chr22:39711548-39711548	p.P172T	1
chr22:39713581-39713581	p.M84V	1
chr22:39709261-39709261	p.I368V	1
chr22:39710727-39710727	p.Q271Q	1
chr22:39712780-39712780	p.K144K	1
chr22:39713638-39713639	p.?	1
chr22:39709298-39709298	p.T355T	1
chr22:39710735-39710735	p.A269S	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	3	1		7					4	1		3	1				4	2		4
# mutation	3	1		7					4	1		3	1				4	2		4
nonsynonymous SNV	1			6					2	1		1					2	2		2
synonymous SNV	2	1		1					2			2	1				2			2

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
chr22:39713525	p.F102F,RPL3	2
chr22:39709298	p.K143N	1
chr22:39711444	p.T355T,RPL3	1
chr22:39713540	p.D141G	1
chr22:39709650	p.T346A,RPL3	1
chr22:39711492	p.K136T	1
chr22:39713544	p.G339G,RPL3	1
chr22:39709669	p.K135N	1
chr22:39711522	p.V321D,RPL3	1
chr22:39714449	p.K124T,RPL3	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 RPL3 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 RPL3

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


C1QTNF9B,CT45A1,CT45A3,DHRS2,FRG2B,GABPB1,HGC6.3, LOC643008,MAGEA8,MAGEB18,MAGEB2,RGS5,RPL3L,SPPL2A, SUMO2,TYRP1,UGT2B10,UGT2B15,USP29,USP8,ZIM3	ACTA1,ATP2A1,MIR1-1HG,CKM,CSRP3,LMOD2,LOC151300, MYBPC2,MYH2,MYH6,MYH7,MYL1,MYL2,MYLPF, NEB,NRAP,OR5H15,P2RX6P,PPP1R3A,RPL3L,XIRP2

PPP1R17,LINC00588,CACNG7,CER1,CHRNA4,CPLX3,FAM27L, LHX3,PAQR9,RBMY1A3P,RPL3L,SHISA7,SLC1A6,SLC6A5, TFAP2D,TSPY1,TSPY4,UNCX	ACTBL2,LINC00596,SCP2D1,DUOX1,FAM74A1,FAM92A1P2,FLJ25758, GAL,HELT,KRTAP13-1,LY6D,MCHR1,OR1J2,PFN3, PRAMEF12,RBMXL3,RPL3L,SNORA64,SNORA74A,tAKR,TM4SF19, TRIM42,USP26,VWCE,X

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 RPL3

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 L3	experimental	Alpha-Hydroxy-Beta-Phenyl-Propionic Acid
DB07374	ribosomal protein L3	experimental	ANISOMYCIN
DB08437	ribosomal protein L3	experimental	PUROMYCIN

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Cross referenced IDs for RPL3

* 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