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 RPL28

Basic gene info.	Gene symbol	RPL28
	Gene name	ribosomal protein L28
	Synonyms	L28
	Cytomap	UCSC genome browser: 19q13.4
	Genomic location	chr19 :55897299-55903451
	Type of gene	protein-coding
	RefGenes	NM_000991.4, NM_001136134.1,NM_001136135.1,NM_001136136.1,NM_001136137.1,
	Ensembl id	ENSG00000108107
	Description	60S ribosomal protein L28
	Modification date	20141207
dbXrefs	MIM : 603638
	HGNC : HGNC
	Ensembl : ENSG00000108107
	HPRD : 04702
	Vega : OTTHUMG00000171991
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPL28
	BioGPS: 6158
	Gene Expression Atlas: ENSG00000108107
	The Human Protein Atlas: ENSG00000108107
Pathway	NCI Pathway Interaction Database: RPL28
	KEGG: RPL28
	REACTOME: RPL28
	ConsensusPathDB
	Pathway Commons: RPL28
Metabolism	MetaCyc: RPL28
	HUMANCyc: RPL28
Regulation	Ensembl's Regulation: ENSG00000108107
	miRBase: chr19 :55,897,299-55,903,451
	TargetScan: NM_000991
	cisRED: ENSG00000108107
Context	iHOP: RPL28
	cancer metabolism search in PubMed: RPL28
	UCL Cancer Institute: RPL28
Assigned class in ccmGDB	C

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Phenotypic Information for RPL28(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RPL28
	Familial Cancer Database: RPL28

* 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: RPL28
	MedGen: RPL28 (Human Medical Genetics with Condition)
	ClinVar: RPL28
Phenotype	MGI: RPL28 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RPL28

Mutations for RPL28

* 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 RPL28 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
DA524376	RPL28	1	366	19	55897300	55899416	GLB1	366	510	3	33114063	33114206
BE388585	RPL28	4	57	19	55897722	55897775	LASP1	53	366	17	37076280	37076593
BE387849	RPL28	3	56	19	55897722	55897775	LASP1	52	366	17	37076280	37076593
BG748632	RPL28	1	601	19	55897314	55899746	ZNF804B	590	611	7	88482050	88482071
AW498880	RPL28	1	160	19	55899375	55899730	GAPDH	161	391	12	6644002	6645955
BQ653766	BCYRN1	1	643	X	70514085	70517282	RPL28	636	690	19	55899686	55899740
BC004230	RPL28	44	532	19	55897311	55899744	TPI1	529	1753	12	6976702	6979993
AA776201	RPL28	1	106	19	55899611	55899717	EPB41L1	106	374	20	34773218	34776411
BQ648662	CBWD2	21	56	2	114223330	114223370	RPL28	39	504	19	55897717	55899743
BC009885	RPL28	44	532	19	55897311	55899744	TPI1	529	1753	12	6976702	6979993
BQ645838	CBWD2	21	56	2	114223330	114223370	RPL28	39	504	19	55897717	55899743
BU543829	ANGPTL4	40	767	19	8436347	8439255	RPL28	768	885	19	55897312	55897809
BG473709	DDX1	17	290	2	15760492	15767242	RPL28	272	739	19	55897300	55899708
BQ646046	CBWD2	22	57	2	114223330	114223370	RPL28	40	505	19	55897717	55899743
AI907286	RPL28	12	158	19	55897736	55898013	RPL28	150	247	19	55898027	55899360
DB253394	RPL28	33	360	19	55897716	55899410	C22orf23	357	559	22	38340103	38340305
BQ649823	CBWD2	22	57	2	114223330	114223370	RPL28	40	505	19	55897717	55899743

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=12)	Stat. for Synonymous SNVs (# total SNVs=2)

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
chr19:55897738-55897738	p.L5V	1
chr19:55899332-55899332	p.T80T	1
chr19:55897765-55897765	p.S14P	1
chr19:55899351-55899351	p.R87S	1
chr19:55897779-55897779	p.I18M	1
chr19:55899356-55899356	p.A88A	1
chr19:55897789-55897789	p.K22E	1
chr19:55899358-55899358	p.T89R	1
chr19:55897997-55897997	p.K47N	1
chr19:55899365-55899365	p.S91R	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			3			2		2			3	1			1	1	1		4
# mutation	1			3			2		2			3	1			1	1	1		4
nonsynonymous SNV	1			3			1		2			2	1			1		1		3
synonymous SNV							1					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
chr19:55897738	p.R87S,RPL28	1
chr19:55899332	p.A88A,RPL28	1
chr19:55897765	p.S91R,RPL28	1
chr19:55899351	p.R103H,RPL28	1
chr19:55897779	p.L5V,RPL28	1
chr19:55899356	p.D105N,RPL28	1
chr19:55897785	p.S14P,RPL28	1
chr19:55899365	p.R130Q	1
chr19:55897789	p.I18M,RPL28	1
chr19:55899400	p.A123V	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 RPL28 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 RPL28

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


ATP5D,FAU,HSPBP1,NDUFA3,RPL13,RPL13A,RPL13AP20, RPL18,RPL28,RPL29,RPL35,RPL36,RPL37A,RPLP2, RPS11,RPS15,RPS19,RPS5,RPS9,ZNF524,ZNF579	DNAJC4,ETHE1,FAU,MRPS2,RPL13,RPL13A,RPL18, RPL18A,RPL19,RPL28,RPL29,RPL35,RPL36,RPP21, RPS15,RPS16,RPS19,RPS21,RPS9,SLC27A5,ZNF581

GLTSCR2,RPL13,RPL13A,RPL18,RPL28,RPL36,RPL38, RPLP0,RPLP2,RPS11,RPS15,RPS16,RPS19,RPS2, RPS3,RPS5,RPS9,SNRPD2,UBA52,ZNF524,ZNF581	ATPAF2,EEF1G,EIF3D,EIF3F,GNB2L1,MACROD1,MAPKAPK3, NOB1,QTRT1,RPL13,RPL18,RPL28,RPL36,RPL37, RPLP2,RPS15,RPS19,RPS2,SLC25A6,UBA52,ZNF524

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 RPL28

There's no related Drug.

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Cross referenced IDs for RPL28

* 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