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 RPS27A

Basic gene info.	Gene symbol	RPS27A
	Gene name	ribosomal protein S27a
	Synonyms	CEP80\|HEL112\|S27A\|UBA80\|UBC\|UBCEP1\|UBCEP80
	Cytomap	UCSC genome browser: 2p16
	Genomic location	chr2 :55459813-55462989
	Type of gene	protein-coding
	RefGenes	NM_001135592.2, NM_001177413.1,NM_002954.5,
	Ensembl id	ENSG00000143947
	Description	40S ribosomal protein S27aepididymis luminal protein 112ubiquitin Cubiquitin and ribosomal protein S27aubiquitin carboxyl extension protein 80ubiquitin-40S ribosomal protein S27aubiquitin-CEP80
	Modification date	20141207
dbXrefs	MIM : 191343
	HGNC : HGNC
	Ensembl : ENSG00000143947
	HPRD : 01878
	Vega : OTTHUMG00000151919
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPS27A
	BioGPS: 6233
	Gene Expression Atlas: ENSG00000143947
	The Human Protein Atlas: ENSG00000143947
Pathway	NCI Pathway Interaction Database: RPS27A
	KEGG: RPS27A
	REACTOME: RPS27A
	ConsensusPathDB
	Pathway Commons: RPS27A
Metabolism	MetaCyc: RPS27A
	HUMANCyc: RPS27A
Regulation	Ensembl's Regulation: ENSG00000143947
	miRBase: chr2 :55,459,813-55,462,989
	TargetScan: NM_001135592
	cisRED: ENSG00000143947
Context	iHOP: RPS27A
	cancer metabolism search in PubMed: RPS27A
	UCL Cancer Institute: RPS27A
Assigned class in ccmGDB	C

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Phenotypic Information for RPS27A(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RPS27A
	Familial Cancer Database: RPS27A

* 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: RPS27A
	MedGen: RPS27A (Human Medical Genetics with Condition)
	ClinVar: RPS27A
Phenotype	MGI: RPS27A (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RPS27A

Mutations for RPS27A

* 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 RPS27A 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
BF375146	RPS27A	9	175	2	55461998	55462629	LIPH	168	499	3	185232431	185232763
DA583490	TOX4	1	103	14	21946363	21946465	RPS27A	100	545	2	55460973	55461418
BM312306	RPS27A	24	193	2	55462574	55462743	UBE3C	189	358	7	156985035	156985204

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=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=3)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=1)

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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
chr2:55462090-55462090	p.Y105H	1
chr2:55460516-55460516	p.T22T	1
chr2:55462091-55462091	p.Y105F	1
chr2:55461266-55461267	p.P38_D39insG	1
chr2:55462094-55462094	p.Y106C	1
chr2:55461267-55461268	p.D39>ES	1
chr2:55462554-55462554	p.?	1
chr2:55461288-55461288	p.A46V	1
chr2:55462577-55462577	p.G112D	1
chr2:55461327-55461327	p.Y59C	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		1				2		1					1	1		1	1		3
# mutation	1		1				2		1					1	1		1	1		4
nonsynonymous SNV	1						1		1					1	1		1	1		3
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
chr2:55462577	p.T22T,RPS27A	1
chr2:55460509	p.A46V,RPS27A	1
chr2:55460516	p.Y59C,RPS27A	1
chr2:55461288	p.L67V,RPS27A	1
chr2:55461327	p.K94K,RPS27A	1
chr2:55461976	p.K97N,RPS27A	1
chr2:55462059	p.L103M,RPS27A	1
chr2:55462068	p.Y105H,RPS27A	1
chr2:55462084	p.Y105F,RPS27A	1
chr2:55462090	p.G112D,RPS27A	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 RPS27A 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 RPS27A

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


EEF1B2,RPL10A,RPL11,RPL17,RPL27A,RPL31,RPL35A, RPL36,RPL37,RPL37A,RPL5,RPLP2,RPS10,RPS13, RPS17,RPS18,RPS19,RPS27A,RPS7,RPS8,RPSAP58	BTF3,RPL10,RPL14,RPL15,RPL22,RPL23A,RPL24, RPL31,RPL32,RPL34,RPL35A,RPL37,RPL5,RPL6, RPS12,RPS23,RPS27A,RPS3A,RPS4X,RPS6,RPS7

EEF1B2,OLA1,RPL10A,RPL12,RPL14,RPL31,RPL35A, RPL37,RPL37A,RPL6,RPL7A,RPS12,RPS13,RPS17, RPS18,RPS23,RPS24,RPS25,RPS27A,RPS6,RPS7	ALKBH2,EEF1A1,FAU,PFDN5,RPL15,RPL17,RPL24, RPL27,RPL31,RPL34,RPL35A,RPL38,RPL41,RPL5, RPS13,RPS20,RPS23,RPS24,RPS25,RPS27A,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 RPS27A

There's no related Drug.

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Cross referenced IDs for RPS27A

* 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