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 RPS24

Basic gene info.	Gene symbol	RPS24
	Gene name	ribosomal protein S24
	Synonyms	DBA3\|S24
	Cytomap	UCSC genome browser: 10q22
	Genomic location	chr10 :79793517-79816571
	Type of gene	protein-coding
	RefGenes	NM_001026.4, NM_001142282.1,NM_001142283.1,NM_001142284.1,NM_001142285.1, NM_033022.3,
	Ensembl id	ENSG00000138326
	Description	40S ribosomal protein S24
	Modification date	20141219
dbXrefs	MIM : 602412
	HGNC : HGNC
	Ensembl : ENSG00000138326
	HPRD : 03877
	Vega : OTTHUMG00000018549
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPS24
	BioGPS: 6229
	Gene Expression Atlas: ENSG00000138326
	The Human Protein Atlas: ENSG00000138326
Pathway	NCI Pathway Interaction Database: RPS24
	KEGG: RPS24
	REACTOME: RPS24
	ConsensusPathDB
	Pathway Commons: RPS24
Metabolism	MetaCyc: RPS24
	HUMANCyc: RPS24
Regulation	Ensembl's Regulation: ENSG00000138326
	miRBase: chr10 :79,793,517-79,816,571
	TargetScan: NM_001026
	cisRED: ENSG00000138326
Context	iHOP: RPS24
	cancer metabolism search in PubMed: RPS24
	UCL Cancer Institute: RPS24
Assigned class in ccmGDB	C

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Phenotypic Information for RPS24(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RPS24
	Familial Cancer Database: RPS24

* 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: RPS24
	MedGen: RPS24 (Human Medical Genetics with Condition)
	ClinVar: RPS24
Phenotype	MGI: RPS24 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RPS24

Mutations for RPS24

* 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

There's no inter-chromosomal structural variation.

- 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
pancreas	RPS24	chr10	79801672	79801692		chr10	83618878	83618898
pancreas	RPS24	chr10	79816142	79816162	RPS24	chr10	79816192	79816212

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 RPS24 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
BQ027949	RPS24	18	314	10	79795400	79800455	CLASP1	310	560	2	122122756	122125309
AI908980	RPS23	14	188	5	81573514	81574155	RPS24	189	253	10	79799960	79800413
AW838568	RPS24	66	402	10	79795105	79797006	PMPCB	397	501	7	102963027	102963201
BU153261	IDH1	94	480	2	209104672	209108329	RPS24	471	772	10	79795397	79800459
BG489521	RPS24	10	84	10	79797037	79800399	LUZP1	82	794	1	23420165	23420874
AW838567	RPS24	52	389	10	79795104	79797006	PMPCB	384	488	7	102963027	102963201
BG287995	SMAP2	2	239	1	40882518	40882755	RPS24	231	297	10	79800389	79800455
M31520	RPS27	1	116	1	153964127	153964629	RPS24	106	620	10	79793623	79800460
AA535098	RPS24	1	165	10	79797005	79800454	CTNND1	164	373	11	57575661	57575966
CF130069	RPS24	53	155	10	79799964	79800455	LOC100134368	149	207	16	437240	437298
AI826669	RPS24	2	156	10	79797031	79800455	CLSTN2	152	283	3	139768311	139768442
AI810209	RPS24	2	156	10	79797031	79800455	CLSTN2	152	283	3	139768311	139768442
AW130504	RPS24	1	280	10	79800107	79800385	RPS24	275	340	10	79800088	79800153
BG621223	PAPPA	1	325	9	119139912	119140236	RPS24	313	462	10	79797017	79800454
N33853	RPS24	1	329	10	79795369	79800454	CPEB2	324	390	4	15068957	15069023

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

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=13)	Stat. for Synonymous SNVs (# total SNVs=1)

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
chr10:79797001-79797001	p.R110H	3
chr10:79795125-79795125	p.I7V	2
chr10:79795386-79795386	p.H63Y	1
chr10:79795387-79795387	p.H63R	1
chr10:79795448-79795448	p.K83K	1
chr10:79796969-79796969	p.K99K	1
chr10:79793660-79793660	p.M1L	1
chr10:79796974-79796974	p.K101R	1
chr10:79795119-79795119	p.V5I	1
chr10:79796976-79796976	p.T102A	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				1						1				1			1	2		3
# mutation				1						1				1			1	2		2
nonsynonymous SNV				1						1				1			1	1		2
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
chr10:79797001	p.R110H,RPS24	2
chr10:79814360	p.V5I,RPS24	1
chr10:79795119	p.V35V,RPS24	1
chr10:79795304	p.T38R,RPS24	1
chr10:79795312	p.H63Y,RPS24	1
chr10:79795386	p.K101R,RPS24	1
chr10:79796974	p.N124D,RPS24	1
chr10:79797042	p.K154N	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 RPS24 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 RPS24

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,RPL24,RPL27A,RPL29,RPL31, RPL32,RPL35A,RPL37,RPL38,RPL39,RPL6,RPL7A, RPS11,RPS18,RPS19,RPS24,RPS2,RPS7,RPS8	BTF3,RPL12,RPL22,RPL24,RPL26,RPL27A,RPL30, RPL32,RPL35A,RPL38,RPL41,RPL5,RPL6,RPS11, RPS15A,RPS24,RPS25,RPS29,RPS3A,RPS4X,RPS7

NACA,RPL11,RPL12,RPL14,RPL26,RPL29,RPL31, RPL32,RPL34,RPL35A,RPL37,RPL37A,RPL6,RPL7A, RPS13,RPS18,RPS23,RPS24,RPS25,RPS27A,RPS6	C12orf57,EEF1A1P9,HSCB,MED28,RPL12,RPL15,RPL19, RPL24,RPL32,RPL35A,RPL41,RPL5,RPL6,RPL7, RPL7A,RPS11,RPS13,RPS24,RPS25,RPS6,ZNF22

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 RPS24

There's no related Drug.

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Cross referenced IDs for RPS24

* 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