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 RPL34

Basic gene info.	Gene symbol	RPL34
	Gene name	ribosomal protein L34
	Synonyms	L34
	Cytomap	UCSC genome browser: 4q25
	Genomic location	chr4 :109541748-109551639
	Type of gene	protein-coding
	RefGenes	NM_000995.3, NM_033625.2,
	Ensembl id	ENSG00000109475
	Description	60S ribosomal protein L34leukemia-associated protein
	Modification date	20141207
dbXrefs	HGNC : HGNC
	Ensembl : ENSG00000109475
	HPRD : 17996
	Vega : OTTHUMG00000131839
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPL34
	BioGPS: 6164
	Gene Expression Atlas: ENSG00000109475
	The Human Protein Atlas: ENSG00000109475
Pathway	NCI Pathway Interaction Database: RPL34
	KEGG: RPL34
	REACTOME: RPL34
	ConsensusPathDB
	Pathway Commons: RPL34
Metabolism	MetaCyc: RPL34
	HUMANCyc: RPL34
Regulation	Ensembl's Regulation: ENSG00000109475
	miRBase: chr4 :109,541,748-109,551,639
	TargetScan: NM_000995
	cisRED: ENSG00000109475
Context	iHOP: RPL34
	cancer metabolism search in PubMed: RPL34
	UCL Cancer Institute: RPL34
Assigned class in ccmGDB	C

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Phenotypic Information for RPL34(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RPL34
	Familial Cancer Database: RPL34

* 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: RPL34
	MedGen: RPL34 (Human Medical Genetics with Condition)
	ClinVar: RPL34
Phenotype	MGI: RPL34 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RPL34

Mutations for RPL34

* 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

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	RPL34	chr4	109548351	109548371	LOC285456	chr4	109535847	109535867
pancreas	RPL34	chr4	109544589	109544609	PKHD1L1	chr8	110515488	110515508

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 RPL34 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
BM810873	TP53INP2	10	573	20	33297113	33298208	RPL34	569	649	4	109543688	109543767
AA954224	RPL34	3	161	4	109543745	109546412	IQCJ	149	168	3	158826972	158826991
BF697308	INS-IGF2	1	490	11	2153279	2153766	RPL34	480	536	4	109546339	109546396
AI624448	RPL34	1	109	4	109546303	109546411	NEK7	93	403	1	198290707	198291019
AU126976	RPL34	1	166	4	109541733	109543328	PCCB	166	570	3	135969191	135975471

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=7)	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
chr4:109546291-109546291	p.R93C	1
chr4:109546299-109546299	p.F95F	1
chr4:109546339-109546339	p.A109T	1
chr4:109543139-109543139	p.R8R	1
chr4:109546364-109546364	p.K117I	1
chr4:109543317-109543317	p.A41V	1
chr4:109543328-109543328	p.A45T	1
chr4:109543342-109543342	p.C49C	1
chr4:109543360-109543360	p.G55G	1
chr4:109543717-109543717	p.K71T	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				1	1		1
# mutation				1					2				1				1	1		1
nonsynonymous SNV				1					1									1		1
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
chr4:109543328	p.A45T,RPL34	1
chr4:109543342	p.C49C,RPL34	1
chr4:109543360	p.G55G,RPL34	1
chr4:109543723	p.H73R,RPL34	1
chr4:109546291	p.R93C,RPL34	1
chr4:109546299	p.F95F,RPL34	1
chr4:109546339	p.A109T,RPL34	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 RPL34 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 RPL34

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


NACA,RPL11,RPL12,RPL14,RPL18,RPL24,RPL27A, RPL29,RPL31,RPL32,RPL34,RPL37,RPL37A,RPL6, RPLP2,RPS11,RPS14,RPS23,RPS4X,RPS8,RPS9	BTF3,CCT4,EIF3M,RPL15,RPL22,RPL23A,RPL24, RPL30,RPL32,RPL34,RPL35A,RPL41,RPS13,RPS15A, RPS27A,RPS29,RPS3A,RPS4X,RPS6,RPS7,UXT

RPL10A,RPL12,RPL14,RPL24,RPL29,RPL31,RPL32, RPL34,RPL35A,RPL3,RPL36,RPL37,RPL37A,RPL5, RPL7A,RPS11,RPS13,RPS23,RPS25,RPS2,RPS8	BOD1,DPH5,EEF1A1,EIF3E,RPL15,RPL24,RPL26, RPL34,RPL35A,RPL5,RPS12,RPS13,RPS15A,RPS25, RPS3A,RPS6,RPS8,TATDN1,TIMM9,TMEM182,ZFAND1

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 RPL34

There's no related Drug.

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Cross referenced IDs for RPL34

* 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