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 RPL14

Basic gene info.	Gene symbol	RPL14
	Gene name	ribosomal protein L14
	Synonyms	CAG-ISL-7\|CTG-B33\|L14\|RL14\|hRL14
	Cytomap	UCSC genome browser: 3p22-p21.2
	Genomic location	chr3 :40498829-40503859
	Type of gene	protein-coding
	RefGenes	NM_001034996.2, NM_003973.4,
	Ensembl id	ENSG00000188846
	Description	60S ribosomal protein L14
	Modification date	20141207
dbXrefs	HGNC : HGNC
	Ensembl : ENSG00000188846
	HPRD : 10617
	Vega : OTTHUMG00000156046
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPL14
	BioGPS: 9045
	Gene Expression Atlas: ENSG00000188846
	The Human Protein Atlas: ENSG00000188846
Pathway	NCI Pathway Interaction Database: RPL14
	KEGG: RPL14
	REACTOME: RPL14
	ConsensusPathDB
	Pathway Commons: RPL14
Metabolism	MetaCyc: RPL14
	HUMANCyc: RPL14
Regulation	Ensembl's Regulation: ENSG00000188846
	miRBase: chr3 :40,498,829-40,503,859
	TargetScan: NM_001034996
	cisRED: ENSG00000188846
Context	iHOP: RPL14
	cancer metabolism search in PubMed: RPL14
	UCL Cancer Institute: RPL14
Assigned class in ccmGDB	C

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Phenotypic Information for RPL14(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RPL14
	Familial Cancer Database: RPL14

* 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: RPL14
	MedGen: RPL14 (Human Medical Genetics with Condition)
	ClinVar: RPL14
Phenotype	MGI: RPL14 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RPL14

Mutations for RPL14

* 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 RPL14 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
BG519661	RPL14	2	76	3	40503567	40503641	MED12	71	399	X	70361761	70362299
BP334301	RPL14	1	399	3	40498801	40503146	SENP6	390	579	6	76411705	76411897
BC051312	NCOR2	1	1589	12	124904505	124979906	RPL14	1589	1817	3	40503539	40503767
BC033087	NCOR2	1	1752	12	124904505	125002840	RPL14	1752	1975	3	40503542	40503765
AA912468	RPL14	24	95	3	40503696	40503767	H19	92	315	11	2018434	2018658
BC010079	E2F4	10	965	16	67226088	67229791	RPL14	957	1174	3	40503542	40503759
AV738739	RPL14	2	264	3	40503478	40503739	RPL14	265	395	3	40502898	40503136
BU608656	RPL14	13	57	3	40503457	40503501	RPL14	49	346	3	40503485	40503767
CD251046	POMC	1	217	2	25387510	25391431	RPL14	212	446	3	40503530	40503764
BU630143	RPL14	14	251	3	40503534	40503771	S100A16	245	716	1	153579639	153580112

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=0

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=0)	Stat. for Synonymous SNVs (# total SNVs=0)
There's no ns-snv.	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

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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				3	1							4	1				1	1		2
# mutation				3	1							4	1				1	1		2
nonsynonymous SNV				2								3	1				1			2
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
chr3:40499409	p.R11L,RPL14	2
chr3:40499407	p.P19H,RPL14	1
chr3:40499433	p.A49A,RPL14	1
chr3:40500174	p.A76T,RPL14	1
chr3:40502923	p.R90Q,RPL14	1
chr3:40502966	p.R121R,RPL14	1
chr3:40503438	p.A169A,RPL14	1
chr3:40503582	p.P179S,RPL14	1
chr3:40503610	p.A183T,RPL14	1
chr3:40503622	p.A188V,RPL14	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 RPL14 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 RPL14

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,RPL14,RPL15,RPL18,RPL24, RPL27A,RPL29,RPL32,RPL34,RPL37,RPL37A,RPLP1, RPLP2,RPS14,RPS23,RPS2,RPS8,RPSA,RPSAP58	EEF1B2,GNB2L1,RPL10,RPL10A,RPL12,RPL14,RPL29, RPL32,RPL37,RPL4,RPL5,RPL6,RPL7A,RPLP0, RPS11,RPS14,RPS2,RPS6,RPS7,RPS8,RPSAP58

GNB2L1,RPL12,RPL14,RPL15,RPL24,RPL29,RPL31, RPL32,RPL35A,RPL37,RPL37A,RPL7A,RPS13,RPS14, RPS18,RPS23,RPS25,RPS6,RPS8,RPSA,RPSAP58	EEF1A1,EEF1A1P9,RPL10,RPL14,RPL15,RPL19,RPL29, RPL32,RPL3,RPL38,RPL5,RPL7A,RPLP0,RPLP1, RPS11,RPS12,RPS13,RPS3,RPS5,RPS8,RSL1D1

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 RPL14

There's no related Drug.

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Cross referenced IDs for RPL14

* 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