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 RPL10

Basic gene info.	Gene symbol	RPL10
	Gene name	ribosomal protein L10
	Synonyms	AUTSX5\|DXS648\|DXS648E\|L10\|NOV\|QM
	Cytomap	UCSC genome browser: Xq28
	Genomic location	chrX :153626570-153630680
	Type of gene	protein-coding
	RefGenes	NM_001256577.1, NM_001256580.1,NM_006013.3,
	Ensembl id	ENSG00000268963
	Description	60S ribosomal protein L10Wilms tumor-related proteinlaminin receptor homologtumor suppressor QM
	Modification date	20141219
dbXrefs	MIM : 312173
	HGNC : HGNC
	Ensembl : ENSG00000147403
	HPRD : 02421
	Vega : OTTHUMG00000033189
Protein	UniProt: P27635 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPL10
	BioGPS: 6134
	Gene Expression Atlas: ENSG00000268963
	The Human Protein Atlas: ENSG00000268963
Pathway	NCI Pathway Interaction Database: RPL10
	KEGG: RPL10
	REACTOME: RPL10
	ConsensusPathDB
	Pathway Commons: RPL10
Metabolism	MetaCyc: RPL10
	HUMANCyc: RPL10
Regulation	Ensembl's Regulation: ENSG00000268963
	miRBase: chrX :153,626,570-153,630,680
	TargetScan: NM_001256577
	cisRED: ENSG00000268963
Context	iHOP: RPL10
	cancer metabolism search in PubMed: RPL10
	UCL Cancer Institute: RPL10
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for RPL10(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RPL10
	Familial Cancer Database: RPL10

* 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	300847; phenotype. 312173; gene.
Orphanet	106; Autism.
Disease	KEGG Disease: RPL10
	MedGen: RPL10 (Human Medical Genetics with Condition)
	ClinVar: RPL10
Phenotype	MGI: RPL10 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RPL10

Mutations for RPL10

* 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 RPL10 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
AI698719	RPL10	33	79	X	153629208	153629254	MLL2	70	436	12	49435187	49435977
CB162793	CYB5A	1	305	18	71920789	71928412	RPL10	301	555	X	153630508	153630762
DW421192	RPL10	68	232	X	153627678	153627842	POLA1	231	298	X	24806747	24806814
CB164490	CYB5A	1	305	18	71920789	71928412	RPL10	301	592	X	153630471	153630762
AW581181	RPL10	13	247	X	153628766	153629004	RNF213	234	295	17	78318971	78319032
BQ771607	RPL10	18	72	X	153629200	153629254	CSNK2A2	67	548	16	58195561	58196042
BC015618	RPL10	44	549	X	153628152	153629254	POLA2	550	3007	11	65029451	65065088
AA813916	RPL10	55	107	X	153629200	153629254	SCLY	92	241	2	239007418	239007567
AI499133	RPL10	27	81	X	153629200	153629254	IQGAP2	71	464	5	75715629	75716022

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=18)	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
chr23:153627713-153627713	p.S20P	2
chr23:153628932-153628932	p.R153C	2
chr23:153628221-153628221	p.R90W	1
chr23:153628915-153628915	p.H147R	1
chr23:153627716-153627716	p.R21C	1
chr23:153628224-153628224	p.L91F	1
chr23:153628919-153628919	p.V148V	1
chr23:153627724-153627724	p.C23C	1
chr23:153628228-153628228	p.H92P	1
chr23:153627841-153627841	p.R32R	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	1	3	1		2			1		3	2				4	5		5
# mutation	2	2	1	3	1		2			1		3	2				4	5		7
nonsynonymous SNV	2	1	1	3	1		2			1		2					3	5		4
synonymous SNV		1										1	2				1			3

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
chrX:153628932	p.R117C,RPL10	2
chrX:153629109	p.E151K,RPL10	2
chrX:153627716	p.Q97Q,RPL10	1
chrX:153628196	p.D28N,RPL10	1
chrX:153627724	p.S101S,RPL10	1
chrX:153628224	p.R32R,RPL10	1
chrX:153628938	p.H111R,RPL10	1
chrX:153627737	p.K40R,RPL10	1
chrX:153628232	p.V112V,RPL10	1
chrX:153628945	p.E45G,RPL10	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 RPL10 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 RPL10

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


EEF1A1P9,EEF1B2,GNB2L1,RPL10,RPL10A,RPL11,RPL13A, RPL17,RPL31,RPL3,RPL37A,RPL41,RPL6,RPL7A, RPS10,RPS14,RPS18,RPS23,RPS4X,RPS8,RPS9	EEF1B2,EEF1G,FBL,GNB2L1,RPL10,RPL10A,RPL12, RPL14,RPL5,RPL6,RPL7A,RPLP0,RPS14,RPS18, RPS2,RPS3,RPS4X,RPS5,RPS6,RPS8,RPSAP58

EEF1A1,EEF1B2,RPL10A,RPL12,RPL15,RPL32,RPL36, RPL5,RPL7A,RPS10,RPS11,RPS14,RPS15A,RPS18, RPS23,RPS29,RPS3,RPS3A,RPS6,RPS8,RPS9	BOD1,C12orf57,DPH5,EEF1A1P9,RPL10,RPL10A,RPL15, RPL24,RPL29,RPL32,RPL35A,RPL41,RPL5,RPL7A, RPS11,RPS13,RPS14,RPS3A,RPS5,RPS6,RPS8

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 RPL10

There's no related Drug.

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Cross referenced IDs for RPL10

* 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