Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 RPLP2
Basic gene info.Gene symbolRPLP2
Gene nameribosomal protein, large, P2
SynonymsD11S2243E|LP2|P2|RPP2
CytomapUCSC genome browser: 11p15.5
Genomic locationchr11 :809935-812876
Type of geneprotein-coding
RefGenesNM_001004.3,
Ensembl idENSG00000177600
Description60S acidic ribosomal protein P2acidic ribosomal phosphoprotein P2renal carcinoma antigen NY-REN-44
Modification date20141207
dbXrefs MIM : 180530
HGNC : HGNC
HPRD : 01612
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPLP2
BioGPS: 6181
Gene Expression Atlas: ENSG00000177600
The Human Protein Atlas: ENSG00000177600
PathwayNCI Pathway Interaction Database: RPLP2
KEGG: RPLP2
REACTOME: RPLP2
ConsensusPathDB
Pathway Commons: RPLP2
MetabolismMetaCyc: RPLP2
HUMANCyc: RPLP2
RegulationEnsembl's Regulation: ENSG00000177600
miRBase: chr11 :809,935-812,876
TargetScan: NM_001004
cisRED: ENSG00000177600
ContextiHOP: RPLP2
cancer metabolism search in PubMed: RPLP2
UCL Cancer Institute: RPLP2
Assigned class in ccmGDBC

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Phenotypic Information for RPLP2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPLP2
Familial Cancer Database: RPLP2
* 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS
REACTOME_METABOLISM_OF_MRNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: RPLP2
MedGen: RPLP2 (Human Medical Genetics with Condition)
ClinVar: RPLP2
PhenotypeMGI: RPLP2 (International Mouse Phenotyping Consortium)
PhenomicDB: RPLP2

Mutations for RPLP2
* 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows RPLP2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ027739RPLP21921611812551812874HLA-DPA1212264645132974513349
BF813426RPLP218011809968810241RPLP27816511810304811630
CK725085RPLP21940611810234812875LOC100507412402707?109863110167
CA425105RPLP22233811810303812873CALR333615191305158313054597
CD370735RPLP22143611809999812873RPN14336663128339108128339342
CK725171RPLP21940611810234812875LOC100507412402706?109863110167
AW882330RPLP2105911811595811644LRRC3255449117636867176369065
DB193761RPLP2124511809968811645MED15240477222092284820937156
CB529802RPLP21933611810303812874MNDA3297121158815429158817536
BQ335002LTA4H4114129639485696396821RPLP210437111810308812822
AA733088RPLP2233411810275812874PEG1031645879429623794296378
DB355988RPLP2132711810294812874BOD1L132252441360121413601424
AA367796RPLP2817811812574812870HBB1783021152480045248258
BP393246NFYC17414123505841236424RPLP27450011809991812873
BC010093TGFBRAP11019092105889455105946138RPLP21910233111810003812872

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy 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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check002.gifSNV 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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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=3)
Stat. for Synonymous SNVs
(# total SNVs=0)
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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr11:810331-810331p.E33K2
chr11:812614-812614p.A84A1
chr11:812762-812762p.E92Q1
chr11:810334-810334p.A34S1
chr11:812594-812594p.G78C1
chr11:812597-812597p.S79P1

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample 1         1    12  
# mutation 1         1    12  
nonsynonymous SNV 1         1    11  
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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr11:812818p.V71E1
chr11:812574p.G78C1
chr11:812594p.S79P1
chr11:812597p.E92Q1
chr11:812762p.G110G1

check002.gifOther 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

check002.gifCopy Number for RPLP2 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 RPLP2

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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

C19orf43,LSM7,MRPL23,NDUFA11,RPL11,RPL13,RPL18,
RPL24,RPL27A,RPL28,RPL32,RPL35,RPL36,RPL37A,
RPLP1,RPLP2,RPS10,RPS15,RPS19,RPS8,RPS9
BSG,TMEM256,COX4I1,COX6A1,EIF3K,EIF4EBP1,UBALD2,
GLI4,HTRA2,MPST,MRPL10,PCBD1,PQLC1,RPLP2,
RPS16,RPS20,SAT2,SLC25A6,THAP3,TRAPPC2L,USE1

EIF3F,FAU,RPL13,RPL18,RPL28,RPL29,RPL32,
RPL35,RPL36,RPL37A,RPL38,RPLP1,RPLP2,RPS10,
RPS13,RPS15,RPS16,RPS25,RPS2,RPS3,UBA52
EEF1G,GNB2L1,RPL13,RPL18,RPL19,RPL23A,RPL28,
RPL32,RPL36,RPL37,RPL37A,RPL38,RPLP0,RPLP2,
RPS12,RPS15,RPS19,RPS21,RPS29,RPS3,UXT
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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 RPLP2
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB02212ribosomal protein, large, P2experimentalPyrophosphate 2-
DB04137ribosomal protein, large, P2experimentalGuanosine-5'-Triphosphate


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Cross referenced IDs for RPLP2
* 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



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