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 RPL4

Basic gene info.	Gene symbol	RPL4
	Gene name	ribosomal protein L4
	Synonyms	L4
	Cytomap	UCSC genome browser: 15q22
	Genomic location	chr15 :66791652-66797193
	Type of gene	protein-coding
	RefGenes	NM_000968.3,
	Ensembl id	ENSG00000174444
	Description	60S ribosomal protein L160S ribosomal protein L4
	Modification date	20141207
dbXrefs	MIM : 180479
	HGNC : HGNC
	HPRD : 01607
Protein	UniProt: P36578 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPL4
	BioGPS: 6124
	Gene Expression Atlas: ENSG00000174444
	The Human Protein Atlas: ENSG00000174444
Pathway	NCI Pathway Interaction Database: RPL4
	KEGG: RPL4
	REACTOME: RPL4
	ConsensusPathDB
	Pathway Commons: RPL4
Metabolism	MetaCyc: RPL4
	HUMANCyc: RPL4
Regulation	Ensembl's Regulation: ENSG00000174444
	miRBase: chr15 :66,791,652-66,797,193
	TargetScan: NM_000968
	cisRED: ENSG00000174444
Context	iHOP: RPL4
	cancer metabolism search in PubMed: RPL4
	UCL Cancer Institute: RPL4
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for RPL4(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RPL4
	Familial Cancer Database: RPL4

* 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	180479; gene.
Orphanet
Disease	KEGG Disease: RPL4
	MedGen: RPL4 (Human Medical Genetics with Condition)
	ClinVar: RPL4
Phenotype	MGI: RPL4 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RPL4

Mutations for RPL4

* 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 RPL4 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
BU540332	TMSB10	4	164	2	85132778	85133222	RPL4	156	284	15	66791658	66791786
DN601711	RPL4	1	366	15	66794971	66795836	ACTN1	363	748	14	69345177	69347620
DA300676	RPL4	1	83	15	66795163	66795245	LOC653739	84	579	7	134832839	134849481
DA783707	RPL4	1	97	15	66795149	66795245	HS6ST3	97	594	13	97487488	97487986
BG910912	RPL4	1	313	15	66795396	66797157	OGFOD2	314	827	12	123462872	123463558
DB504144	RPL4	2	360	15	66795396	66797205	LOC100505761	361	480	10	104215798	104215917
DB575395	RPL4	1	222	15	66795396	66795810	LOC100505761	223	474	10	104215798	104216049
BU932269	SPCS1	3	121	3	52740135	52740253	RPL4	115	652	15	66793772	66795784
AK290436	TMTC3	1	2907	12	88536073	88589368	RPL4	2900	3004	15	66791661	66791765
BC001010	CDK4	681	772	12	58145029	58145120	RPL4	773	2172	15	66791666	66797165
AV754796	RPL4	27	99	15	66794352	66794428	KRT222	84	284	17	38811870	38812069

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=20)	Stat. for Synonymous SNVs (# total SNVs=7)

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
chr15:66795439-66795439	p.R80Q	2
chr15:66794245-66794245	p.R143C	2
chr15:66795078-66795078	p.G98E	2
chr15:66794220-66794220	p.P151H	1
chr15:66792408-66792408	p.R342C	1
chr15:66795413-66795413	p.Q89E	1
chr15:66793328-66793328	p.Y264Y	1
chr15:66794230-66794230	p.P148S	1
chr15:66792422-66792422	p.R337Q	1
chr15:66793358-66793358	p.E254E	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	2		5			2		2		1	5	3				4	2	1	5
# mutation	2	2		5			2		2		1	5	3				4	2	1	6
nonsynonymous SNV	2	1		4			1		2		1	5	1				3		1	4
synonymous SNV		1		1			1						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
chr15:66795005	p.L322L	1
chr15:66792408	p.R143C	1
chr15:66793735	p.H310R	1
chr15:66795006	p.A135P	1
chr15:66792426	p.K307K	1
chr15:66793741	p.Y122Y	1
chr15:66795050	p.Q299K	1
chr15:66792443	p.Y122F	1
chr15:66793787	p.M284T	1
chr15:66795082	p.T107T	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 RPL4 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 RPL4

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


ATP5G2,NACA,PFDN5,RPL10,RPL10A,RPL11,RPL13A, RPL29,RPL31,RPL34,RPL36,RPL37A,RPL41,RPL7A, RPLP0,RPS14,RPS23,RPS26,RPS29,RPS4X,RPS9	BTF3,CCT4,RPL14,RPL15,RPL23A,RPL24,RPL30, RPL32,RPL35A,RPL37,RPL38,RPL41,RPL6,RPS11, RPS15A,RPS24,RPS2,RPS29,RPS3A,RPS4X,RPS7

EEF1A1,EEF1A1P9,LRRC75A-AS1,PFDN5,RPL10A,RPL13A,RPL18A, RPL36,RPL41,RPLP0,RPS11,RPS14,RPS16,RPS29, RPS3,RPS3A,RPS5,RPS8,RPS9,RPSA,RPSAP58	C12orf57,DPY30,FAU,PFDN5,RPL15,RPL24,RPL27A, RPL35,RPL35A,RPL41,RPL5,RPS11,RPS13,RPS18, RPS3A,RPS5,RPS6,RPS7,RPSAP58,SNRPD2,SSR2

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 RPL4

There's no related Drug.

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Cross referenced IDs for RPL4

* 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