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 RPL27

Basic gene info.	Gene symbol	RPL27
	Gene name	ribosomal protein L27
	Synonyms	L27
	Cytomap	UCSC genome browser: 17q21
	Genomic location	chr17 :41150445-41154971
	Type of gene	protein-coding
	RefGenes	NM_000988.3,
	Ensembl id	ENSG00000131469
	Description	60S ribosomal protein L27
	Modification date	20141207
dbXrefs	MIM : 607526
	HGNC : HGNC
	Ensembl : ENSG00000131469
	HPRD : 09602
	Vega : OTTHUMG00000180660
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPL27
	BioGPS: 6155
	Gene Expression Atlas: ENSG00000131469
	The Human Protein Atlas: ENSG00000131469
Pathway	NCI Pathway Interaction Database: RPL27
	KEGG: RPL27
	REACTOME: RPL27
	ConsensusPathDB
	Pathway Commons: RPL27
Metabolism	MetaCyc: RPL27
	HUMANCyc: RPL27
Regulation	Ensembl's Regulation: ENSG00000131469
	miRBase: chr17 :41,150,445-41,154,971
	TargetScan: NM_000988
	cisRED: ENSG00000131469
Context	iHOP: RPL27
	cancer metabolism search in PubMed: RPL27
	UCL Cancer Institute: RPL27
Assigned class in ccmGDB	C

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Phenotypic Information for RPL27(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RPL27
	Familial Cancer Database: RPL27

* 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: RPL27
	MedGen: RPL27 (Human Medical Genetics with Condition)
	ClinVar: RPL27
Phenotype	MGI: RPL27 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RPL27

Mutations for RPL27

* 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 RPL27 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
EC440105	RPL27	1	48	17	41150801	41150848	NME2	44	96	17	49245608	49245660
EC572330	RPL27	5	51	17	41150802	41150848	NME2	47	99	17	49245608	49245660
DB013482	RPL27	1	450	17	41150452	41154938	KRT13	451	576	17	39661739	39661864
EC578828	RPL27	1	49	17	41150800	41150848	CASP12	37	58	11	104761981	104762002
BU674462	RPL27	8	456	17	41150769	41154976	C1orf210	453	640	1	43747912	43748098
AA503644	OXA1L	1	273	14	23240714	23240992	RPL27	272	485	17	41150760	41152074
CV327307	RPL27	1	339	17	41150760	41154769	RASIP1	334	401	19	49228152	49228219
CV327308	RPL27	1	339	17	41150760	41154769	RASIP1	334	401	19	49228152	49228219
BC021886	RPL27	1	70	17	41154906	41154975	RPL27	66	482	17	41150801	41154976
CV327306	RPL27	1	339	17	41150760	41154769	RASIP1	334	542	19	49228152	49230303
BU685466	RPL27	1	69	17	41154913	41155331	RPL27	65	393	17	41151948	41154934
T59674	RPS6	1	150	9	19376253	19376507	RPL27	150	432	17	41150472	41152121
FJ655906	RPL27	11	345	17	41150760	41154765	NME2	345	395	17	49248882	49248932

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=8)	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
chr17:41152038-41152038	p.M57K	2
chr17:41151975-41151975	p.R36H	1
chr17:41152027-41152027	p.V53V	1
chr17:41152055-41152055	p.A63S	1
chr17:41152077-41152077	p.S70F	1
chr17:41152095-41152095	p.N76S	1
chr17:41154694-41154694	p.S86T	1
chr17:41154751-41154751	p.A105S	1
chr17:41154776-41154776	p.E113G	1
chr17:41151963-41151963	p.G32D	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					2								3			2
# mutation			1	1					2								3			2
nonsynonymous SNV			1	1					2								3			2
synonymous SNV

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
chr17:41152038	p.M57T	2
chr17:41152077	p.R36H	1
chr17:41154694	p.S70F	1
chr17:41154751	p.S86T	1
chr17:41154776	p.A105S	1
chr17:41154798	p.E113G	1
chr17:41151974	p.E120D	1
chr17:41151975	p.R36C	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 RPL27 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 RPL27

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


EIF3F,RPL11,RPL13,RPL14,RPL18,RPL24,RPL27A, RPL31,RPL32,RPL36,RPL37,RPL37A,RPLP2,RPS10, RPS11,RPS13,RPS18,RPS19,RPS2,RPS8,RPS9	NME2,PFDN5,RPL10,RPL11,RPL12,RPL13,RPL18, RPL24,RPL27A,RPL36,RPL38,RPL7A,RPL8,RPLP1, RPS11,RPS14,RPS24,RPS3,RPS8,SNRPD2,SNRPF

AKIP1,LCN15,RPL14,RPL24,RPL27A,RPL29,RPL32, RPL35A,RPL7A,RPS11,RPS13,RPS14,RPS15A,RPS18, RPS25,RPS3,RPS9,RPSA,RPSAP58,TMEM9B,TSSC4	TMEM261,DPY30,EEF1B2,HSCB,LSM2,RPL24,RPL27A, RPL35,RPL35A,RPL41,RPS10,RPS11,RPS13,RPS14, RPS18,RPS3A,RPS5,RPS6,RPS7,RPS8,SNRPD2

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 RPL27

There's no related Drug.

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Cross referenced IDs for RPL27

* 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