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 RPS4X

Basic gene info.	Gene symbol	RPS4X
	Gene name	ribosomal protein S4, X-linked
	Synonyms	CCG2\|DXS306\|RPS4\|S4\|SCAR\|SCR10
	Cytomap	UCSC genome browser: Xq13.1
	Genomic location	chrX :71492452-71497141
	Type of gene	protein-coding
	RefGenes	NM_001007.4,
	Ensembl id	ENSG00000198034
	Description	40S ribosomal protein S4, X isoformcell cycle gene 2ribosomal protein S4X isoformsingle copy abundant mRNA proteinsingle-copy abundant mRNA
	Modification date	20141207
dbXrefs	MIM : 312760
	HGNC : HGNC
	HPRD : 02427
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPS4X
	BioGPS: 6191
	Gene Expression Atlas: ENSG00000198034
	The Human Protein Atlas: ENSG00000198034
Pathway	NCI Pathway Interaction Database: RPS4X
	KEGG: RPS4X
	REACTOME: RPS4X
	ConsensusPathDB
	Pathway Commons: RPS4X
Metabolism	MetaCyc: RPS4X
	HUMANCyc: RPS4X
Regulation	Ensembl's Regulation: ENSG00000198034
	miRBase: chrX :71,492,452-71,497,141
	TargetScan: NM_001007
	cisRED: ENSG00000198034
Context	iHOP: RPS4X
	cancer metabolism search in PubMed: RPS4X
	UCL Cancer Institute: RPS4X
Assigned class in ccmGDB	C

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Phenotypic Information for RPS4X(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RPS4X
	Familial Cancer Database: RPS4X

* 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: RPS4X
	MedGen: RPS4X (Human Medical Genetics with Condition)
	ClinVar: RPS4X
Phenotype	MGI: RPS4X (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RPS4X

Mutations for RPS4X

* 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 RPS4X 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
BF812451	SPTBN1	2	214	2	54882310	54885078	RPS4X	205	447	X	71492479	71493180
BQ305779	RPS4X	10	100	X	71494910	71495001	AHSA1	93	403	14	77935503	77935813
AW015878	RPS4X	19	97	X	71492463	71492541	SUPT5H	94	418	19	39962318	39963718
BF814512	NUP210	41	487	3	13393247	13395161	RPS4X	486	544	X	71493766	71493824
AA075606	GIT2	1	197	12	110423455	110423653	RPS4X	198	587	X	71493161	71495428
BQ325055	SPTBN1	73	251	2	54883049	54885078	RPS4X	242	488	X	71492475	71493180
BG151410	EPHB4	59	128	7	100410417	100410486	RPS4X	125	175	X	71492453	71492503
BF446002	RPS4X	16	94	X	71492456	71492534	RPS4X	91	673	X	71493212	71497068
AI382716	RPS4X	10	64	X	71492453	71492507	ALG10B	62	205	12	38716185	38716327
BF326184	RPS4X	1	134	X	71493086	71493219	RPS4X	131	361	X	71494951	71495573
H21354	RPS4X	7	101	X	71492469	71492563	ZNF24	98	440	18	32920252	32920592

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=1)	Stat. for Synonymous SNVs (# total SNVs=0)
	There's no s-snv.
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
chr23:71493138-71493138	p.D212H	1
chr23:71495495-71495495	p.Y54C	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	1	5	1				1			1								2
# mutation	2	2	1	5	1				1			1								2
nonsynonymous SNV	1	2	1	3	1							1
synonymous SNV	1			2					1											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
chrX:71495568	p.V210M	1
chrX:71493144	p.V207M	1
chrX:71496026	p.I154I	1
chrX:71493153	p.P150P	1
chrX:71496038	p.L139M	1
chrX:71493721	p.K120N	1
chrX:71493733	p.I102M	1
chrX:71493768	p.E97E	1
chrX:71494903	p.Y54C	1
chrX:71494957	p.T33T	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 RPS4X 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 RPS4X

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


GNB2L1,NACA,RPL10,RPL10A,RPL11,RPL12,RPL14, RPL15,RPL17,RPL29,RPL31,RPL32,RPL34,RPL3, RPL6,RPL7A,RPS14,RPS18,RPS23,RPS4X,RPS8	BTF3,CCT4,FBL,GNB2L1,RPL10A,RPL12,RPL14, RPL22,RPL24,RPL32,RPL35A,RPL41,RPL5,RPL6, RPS24,RPS27A,RPS3A,RPS4X,RPS6,RPS7,RPS8

EIF1AX,EIF2S3,FAM104B,IGBP1,NDUFB11,PQBP1,RBM3, RBMX2,RPL10,RPL10A,RPL12,RPL32,RPL37,RPL5, RPL7A,RPS23,RPS25,RPS4X,RPS8,SLC25A6,UXT	EEF1G,EIF1AX,EIF3H,GNB2L1,MACROD1,JPX,PNPLA4, RPL10,RPL13,RPL13A,RPL14,RPL18,RPL30,RPL32, RPL3,RPL36,RPL37A,RPL38,RPL7A,RPS12,RPS4X

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 RPS4X

There's no related Drug.

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Cross referenced IDs for RPS4X

* 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