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 RPLP2

Basic gene info.	Gene symbol	RPLP2
	Gene name	ribosomal protein, large, P2
	Synonyms	D11S2243E\|LP2\|P2\|RPP2
	Cytomap	UCSC genome browser: 11p15.5
	Genomic location	chr11 :809935-812876
	Type of gene	protein-coding
	RefGenes	NM_001004.3,
	Ensembl id	ENSG00000177600
	Description	60S acidic ribosomal protein P2acidic ribosomal phosphoprotein P2renal carcinoma antigen NY-REN-44
	Modification date	20141207
dbXrefs	MIM : 180530
	HGNC : HGNC
	HPRD : 01612
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPLP2
	BioGPS: 6181
	Gene Expression Atlas: ENSG00000177600
	The Human Protein Atlas: ENSG00000177600
Pathway	NCI Pathway Interaction Database: RPLP2
	KEGG: RPLP2
	REACTOME: RPLP2
	ConsensusPathDB
	Pathway Commons: RPLP2
Metabolism	MetaCyc: RPLP2
	HUMANCyc: RPLP2
Regulation	Ensembl's Regulation: ENSG00000177600
	miRBase: chr11 :809,935-812,876
	TargetScan: NM_001004
	cisRED: ENSG00000177600
Context	iHOP: RPLP2
	cancer metabolism search in PubMed: RPLP2
	UCL Cancer Institute: RPLP2
Assigned class in ccmGDB	C

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Phenotypic Information for RPLP2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RPLP2
	Familial Cancer Database: RPLP2

* 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: RPLP2
	MedGen: RPLP2 (Human Medical Genetics with Condition)
	ClinVar: RPLP2
Phenotype	MGI: RPLP2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RPLP2

Mutations for RPLP2

* 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 RPLP2 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
BQ027739	RPLP2	19	216	11	812551	812874	HLA-DPA1	212	264	6	4513297	4513349
BF813426	RPLP2	1	80	11	809968	810241	RPLP2	78	165	11	810304	811630
CK725085	RPLP2	19	406	11	810234	812875	LOC100507412	402	707	?	109863	110167
CA425105	RPLP2	22	338	11	810303	812873	CALR	333	615	19	13051583	13054597
CD370735	RPLP2	21	436	11	809999	812873	RPN1	433	666	3	128339108	128339342
CK725171	RPLP2	19	406	11	810234	812875	LOC100507412	402	706	?	109863	110167
AW882330	RPLP2	10	59	11	811595	811644	LRRC32	55	449	11	76368671	76369065
DB193761	RPLP2	1	245	11	809968	811645	MED15	240	477	22	20922848	20937156
CB529802	RPLP2	19	336	11	810303	812874	MNDA	329	712	1	158815429	158817536
BQ335002	LTA4H	4	114	12	96394856	96396821	RPLP2	104	371	11	810308	812822
AA733088	RPLP2	2	334	11	810275	812874	PEG10	316	458	7	94296237	94296378
DB355988	RPLP2	1	327	11	810294	812874	BOD1L1	322	524	4	13601214	13601424
AA367796	RPLP2	8	178	11	812574	812870	HBB	178	302	11	5248004	5248258
BP393246	NFYC	1	74	1	41235058	41236424	RPLP2	74	500	11	809991	812873
BC010093	TGFBRAP1	10	1909	2	105889455	105946138	RPLP2	1910	2331	11	810003	812872

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=3)	Stat. for Synonymous SNVs (# total SNVs=0)
	There's no s-snv.
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
chr11:810331-810331	p.E33K	2
chr11:812762-812762	p.E92Q	1
chr11:810334-810334	p.A34S	1
chr11:812594-812594	p.G78C	1
chr11:812597-812597	p.S79P	1
chr11:812614-812614	p.A84A	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										1					1	2
# mutation		1										1					1	2
nonsynonymous SNV		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
chr11:812574	p.V71E	1
chr11:812594	p.G78C	1
chr11:812597	p.S79P	1
chr11:812762	p.E92Q	1
chr11:812818	p.G110G	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 RPLP2 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 RPLP2

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


C19orf43,LSM7,MRPL23,NDUFA11,RPL11,RPL13,RPL18, RPL24,RPL27A,RPL28,RPL32,RPL35,RPL36,RPL37A, RPLP1,RPLP2,RPS10,RPS15,RPS19,RPS8,RPS9	BSG,TMEM256,COX4I1,COX6A1,EIF3K,EIF4EBP1,UBALD2, GLI4,HTRA2,MPST,MRPL10,PCBD1,PQLC1,RPLP2, RPS16,RPS20,SAT2,SLC25A6,THAP3,TRAPPC2L,USE1

EIF3F,FAU,RPL13,RPL18,RPL28,RPL29,RPL32, RPL35,RPL36,RPL37A,RPL38,RPLP1,RPLP2,RPS10, RPS13,RPS15,RPS16,RPS25,RPS2,RPS3,UBA52	EEF1G,GNB2L1,RPL13,RPL18,RPL19,RPL23A,RPL28, RPL32,RPL36,RPL37,RPL37A,RPL38,RPLP0,RPLP2, RPS12,RPS15,RPS19,RPS21,RPS29,RPS3,UXT

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 RPLP2

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
DB02212	ribosomal protein, large, P2	experimental	Pyrophosphate 2-
DB04137	ribosomal protein, large, P2	experimental	Guanosine-5'-Triphosphate

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Cross referenced IDs for RPLP2

* 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