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 RPL30

Basic gene info.	Gene symbol	RPL30
	Gene name	ribosomal protein L30
	Synonyms	L30
	Cytomap	UCSC genome browser: 8q22
	Genomic location	chr8 :99053937-99057818
	Type of gene	protein-coding
	RefGenes	NM_000989.3,
	Ensembl id	ENSG00000156482
	Description	60S ribosomal protein L30
	Modification date	20141207
dbXrefs	MIM : 180467
	HGNC : HGNC
	Ensembl : ENSG00000156482
	HPRD : 01595
	Vega : OTTHUMG00000164796
Protein	UniProt: P62888 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPL30
	BioGPS: 6156
	Gene Expression Atlas: ENSG00000156482
	The Human Protein Atlas: ENSG00000156482
Pathway	NCI Pathway Interaction Database: RPL30
	KEGG: RPL30
	REACTOME: RPL30
	ConsensusPathDB
	Pathway Commons: RPL30
Metabolism	MetaCyc: RPL30
	HUMANCyc: RPL30
Regulation	Ensembl's Regulation: ENSG00000156482
	miRBase: chr8 :99,053,937-99,057,818
	TargetScan: NM_000989
	cisRED: ENSG00000156482
Context	iHOP: RPL30
	cancer metabolism search in PubMed: RPL30
	UCL Cancer Institute: RPL30
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for RPL30(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RPL30
	Familial Cancer Database: RPL30

* 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	180467; gene.
Orphanet
Disease	KEGG Disease: RPL30
	MedGen: RPL30 (Human Medical Genetics with Condition)
	ClinVar: RPL30
Phenotype	MGI: RPL30 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RPL30

Mutations for RPL30

* 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 RPL30 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
CD389544	CACNA1E	238	257	1	181611728	181611747	RPL30	256	516	8	99053949	99055003
BU526643	RPL30	1	461	8	99053947	99057626	PRKCZ	442	461	1	2065738	2065757
BU526580	RPL30	1	461	8	99053947	99057626	PRKCZ	442	461	1	2065738	2065757
DB125840	RPL30	1	91	8	99057575	99057773	TBC1D5	91	530	3	17279809	17349627
AW662691	TP53BP2	8	295	1	223967790	223968077	RPL30	295	508	8	99057180	99057760
BC008012	RPL30	43	415	8	99053949	99057600	EEF1D	407	1377	8	144661898	144679574
AA315842	RPL30	4	65	8	99054032	99054887	REG4	66	462	1	120342385	120354068
BI334582	NOP58	1	380	2	203149104	203155926	RPL30	380	735	8	99054882	99057760
BG180512	TTC37	1	89	5	94861108	94861196	RPL30	79	473	8	99053569	99057248
BU608418	RPL30	1	76	8	99053569	99054011	RPL30	74	219	8	99054000	99054939
BF923959	MEGF11	8	152	15	66459159	66459306	RPL30	139	437	8	99054942	99057773
BQ221159	RPL30	1	56	8	99054945	99055000	KCTD18	52	217	2	201353675	201353840

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=1

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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=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
chr8:99054041-99054041	p.T112T	1
chr8:99054891-99054891	p.L94V	1
chr8:99054939-99054939	p.N78D	1
chr8:99057209-99057209	p.A43A	1
chr8:99057222-99057222	p.R39K	1
chr8:99057237-99057237	p.T34I	1
chr8:99057245-99057245	p.Y31*	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									2			2	2				1
# mutation									2			3	2				1
nonsynonymous SNV									2			3	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
chr8:99054891	p.L94V	1
chr8:99054939	p.N78D	1
chr8:99054972	p.A67S	1
chr8:99057180	p.P53Q	1
chr8:99057209	p.A43A	1
chr8:99057237	p.T34I	1
chr8:99057250	p.G30W	1
chr8:99057265	p.G25W	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 RPL30 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 RPL30

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


C8orf59,CYC1,EEF1D,ENY2,EXOSC4,LOC442454,MAF1, PUF60,RPL27A,RPL30,RPL37A,RPL8,RPLP2,RPS10, RPS20,RPS8,RRS1,SNHG6,TCEB1,TOP1MT,UQCRB	BTF3,RPL10,RPL22,RPL23A,RPL24,RPL30,RPL32, RPL35A,RPL37,RPL38,RPL41,RPL6,RPS13,RPS15A, RPS23,RPS24,RPS29,RPS3A,RPS6,RPS7,UXT

ANKRD46,NDUFAF6,C8orf59,COPS5,DCAF13,EBAG9,EEF1D, EIF3E,EIF3H,MED30,MTERF3,NDUFB9,PABPC1,RPL30, RPL8,RPS20,SNHG6,TATDN1,TCEB1,UQCRB,ZFAND1	EEF1A1,RPL10,RPL12,RPL14,RPL15,RPL19,RPL23A, RPL30,RPL31,RPL32,RPL35A,RPL3,RPL38,RPL6, RPL7A,RPS11,RPS12,RPS13,RPS23,RPS25,RPS9

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 RPL30

There's no related Drug.

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Cross referenced IDs for RPL30

* 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