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 RPL11

Basic gene info.	Gene symbol	RPL11
	Gene name	ribosomal protein L11
	Synonyms	DBA7\|GIG34\|L11
	Cytomap	UCSC genome browser: 1p36.1-p35
	Genomic location	chr1 :24018268-24022915
	Type of gene	protein-coding
	RefGenes	NM_000975.3, NM_001199802.1,
	Ensembl id	ENSG00000142676
	Description	60S ribosomal protein L11CLL-associated antigen KW-12cell growth-inhibiting protein 34
	Modification date	20141222
dbXrefs	MIM : 604175
	HGNC : HGNC
	Ensembl : ENSG00000142676
	HPRD : 10364
	Vega : OTTHUMG00000002926
Protein	UniProt: P62913 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPL11
	BioGPS: 6135
	Gene Expression Atlas: ENSG00000142676
	The Human Protein Atlas: ENSG00000142676
Pathway	NCI Pathway Interaction Database: RPL11
	KEGG: RPL11
	REACTOME: RPL11
	ConsensusPathDB
	Pathway Commons: RPL11
Metabolism	MetaCyc: RPL11
	HUMANCyc: RPL11
Regulation	Ensembl's Regulation: ENSG00000142676
	miRBase: chr1 :24,018,268-24,022,915
	TargetScan: NM_000975
	cisRED: ENSG00000142676
Context	iHOP: RPL11
	cancer metabolism search in PubMed: RPL11
	UCL Cancer Institute: RPL11
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for RPL11(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RPL11
	Familial Cancer Database: RPL11

* 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	604175; gene. 612562; phenotype.
Orphanet	124; Blackfan-Diamond anemia.
Disease	KEGG Disease: RPL11
	MedGen: RPL11 (Human Medical Genetics with Condition)
	ClinVar: RPL11
Phenotype	MGI: RPL11 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RPL11

Mutations for RPL11

* 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 RPL11 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
AA447363	RPL11	1	174	1	24022300	24022908	KDM5C	170	448	X	53222271	53222655
CN269184	RPL11	1	438	1	24019100	24022336	TMCO6	433	545	5	140021281	140021725
CB409379	RPL11	1	487	1	24019108	24022397	NDUFB4	485	573	3	120321083	120321171
AU134575	RPL11	1	494	1	24018296	24022367	STRN4	489	647	19	47226479	47228158
BE613010	RPL11	14	96	1	24020323	24020406	EPHX1	97	687	1	226027547	226033006
BQ310852	RPL11	1	70	1	24019146	24019217	RPL11	66	403	1	24019218	24022354
CD388242	RPL11	41	302	1	24019098	24020406	TKT	302	386	3	53259668	53259752
BU598868	NAA50	1	559	3	113442278	113465099	RPL11	556	732	1	24022297	24022905
AU100496	FRYL	58	77	4	48531050	48531069	RPL11	68	300	1	24019132	24020764
CV387556	ADAMTS2	111	130	5	178701856	178701875	RPL11	131	544	1	24018296	24021281

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=17)	Stat. for Synonymous SNVs (# total SNVs=3)

Stat. for Deletions (# total SNVs=1)	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
chr1:24021260-24021260	p.I125M	3
chr1:24019138-24019138	p.R16C	2
chr1:24022315-24022315	p.A142T	2
chr1:24019220-24019220	p.L43H	2
chr1:24018320-24018320	p.?	2
chr1:24020362-24020362	p.R75*	2
chr1:24022834-24022835	p.Y170fs*1	1
chr1:24019129-24019129	p.R13W	1
chr1:24021182-24021182	p.F99F	1
chr1:24022839-24022839	p.D171D	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	2			4					1	1		2					1			4
# mutation	2			4					1	1		2					1			4
nonsynonymous SNV	2			3					1	1		1					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
chr1:24022315	p.A142T,RPL11	2
chr1:24019138	p.R16C,RPL11	1
chr1:24022839	p.S59F,RPL11	1
chr1:24020315	p.S100L,RPL11	1
chr1:24022845	p.F107V,RPL11	1
chr1:24021184	p.G108G,RPL11	1
chr1:24021204	p.I125M,RPL11	1
chr1:24021209	p.D129V,RPL11	1
chr1:24021260	p.R146H,RPL11	1
chr1:24021271	p.I151F,RPL11	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 RPL11 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 RPL11

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


RPL11,RPL12,RPL18,RPL24,RPL27A,RPL29,RPL31, RPL32,RPL34,RPL36,RPL37,RPL37A,RPL6,RPL7A, RPLP2,RPS11,RPS14,RPS18,RPS23,RPS8,RPS9	RPL10,RPL11,RPL14,RPL19,RPL24,RPL27A,RPL29, RPL35,RPL36,RPL37,RPL38,RPL5,RPL6,RPL7A, RPS11,RPS14,RPS16,RPS17,RPS25,RPS6,RPS8

PITHD1,GNB2L1,NACA,RPL11,RPL12,RPL22,RPL26, RPL31,RPL34,RPL35A,RPL3,RPL37,RPL37A,RPL6, RPL7A,RPLP2,RPS24,RPS25,RPS2,RPS27A,SYF2	EIF3H,NACA,RPL10,RPL11,RPL12,RPL14,RPL19, RPL30,RPL31,RPL32,RPL3,RPL4,RPL6,RPL7, RPL7A,RPS12,RPS20,RPS23,RPS24,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 RPL11

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA34664; -.
Organism-specific databases	CTD	6135; -.

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 L11	experimental	Alpha-Hydroxy-Beta-Phenyl-Propionic Acid
DB07374	ribosomal protein L11	experimental	ANISOMYCIN
DB08437	ribosomal protein L11	experimental	PUROMYCIN

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Cross referenced IDs for RPL11

* 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