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 RPL29
Basic gene info.Gene symbolRPL29
Gene nameribosomal protein L29
SynonymsHIP|HUMRPL29|L29|RPL29P10|RPL29_3_370
CytomapUCSC genome browser: 3p21.3-p21.2
Genomic locationchr3 :52027643-52029958
Type of geneprotein-coding
RefGenesNM_000992.2,
Ensembl idENSG00000162244
Description60S ribosomal protein L29HP/HS-interacting proteincell surface heparin-binding protein HIPheparin/heparan sulfate-binding proteinheparin/heparan sulfate-interacting proteinribosomal protein YL43 homologue
Modification date20141207
dbXrefs MIM : 601832
HGNC : HGNC
Ensembl : ENSG00000162244
HPRD : 03495
Vega : OTTHUMG00000155262
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPL29
BioGPS: 6159
Gene Expression Atlas: ENSG00000162244
The Human Protein Atlas: ENSG00000162244
PathwayNCI Pathway Interaction Database: RPL29
KEGG: RPL29
REACTOME: RPL29
ConsensusPathDB
Pathway Commons: RPL29
MetabolismMetaCyc: RPL29
HUMANCyc: RPL29
RegulationEnsembl's Regulation: ENSG00000162244
miRBase: chr3 :52,027,643-52,029,958
TargetScan: NM_000992
cisRED: ENSG00000162244
ContextiHOP: RPL29
cancer metabolism search in PubMed: RPL29
UCL Cancer Institute: RPL29
Assigned class in ccmGDBC

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Phenotypic Information for RPL29(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPL29
Familial Cancer Database: RPL29
* 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: RPL29
MedGen: RPL29 (Human Medical Genetics with Condition)
ClinVar: RPL29
PhenotypeMGI: RPL29 (International Mouse Phenotyping Consortium)
PhenomicDB: RPL29

Mutations for RPL29
* 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 RPL29 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW860778CD74143855149784690149786889RPL2937453535202905552029930

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=7)
Stat. for Synonymous SNVs
(# total SNVs=2)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr3:52029073-52029073p.Y29*2
chr3:52028047-52028047p.S66S1
chr3:52027797-52027797p.R150G1
chr3:52027815-52027815p.P144S1
chr3:52029107-52029107p.R18K1
chr3:52027853-52027854p.K130_D131insAK1
chr3:52029445-52029445p.N11N1
chr3:52027854-52027859p.A129_K130delAK1
chr3:52027925-52027925p.R107H1
chr3:52027960-52027960p.R95R1

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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  1 12 3
# mutation         1 1  1 12 3
nonsynonymous SNV           1  1 1  2
synonymous SNV         1       2 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
chr3:52029445p.R150G1
chr3:52027797p.P144S1
chr3:52027815p.R111S1
chr3:52027914p.R95R1
chr3:52027960p.L93L1
chr3:52027966p.K73K1
chr3:52028026p.A69T1
chr3:52028040p.S66S1
chr3:52028047p.Y29C1
chr3:52029074p.R18K1

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 RPL29 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 RPL29

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

RPL11,RPL12,RPL14,RPL15,RPL18,RPL24,RPL29,
RPL32,RPL34,RPL35,RPL36,RPL37,RPL37A,RPL7A,
RPLP2,RPS11,RPS14,RPS2,RPS4X,RPS8,RPS9
PHB2,RPL10,RPL13,RPL13A,RPL14,RPL18,RPL18A,
RPL19,RPL29,RPL32,RPL35,RPL36,RPL37,RPL37A,
RPL7A,RPS14,RPS16,RPS2,RPS5,RPS6,RPS8

RPL10A,RPL12,RPL14,RPL15,RPL24,RPL29,RPL32,
RPL35,RPL35A,RPL37A,RPL7A,RPS13,RPS14,RPS15,
RPS18,RPS23,RPS3,RPS8,RPS9,RPSA,RPSAP58
ATP5G2,PHB2,RPL10,RPL10A,RPL13A,RPL14,RPL18,
RPL18A,RPL19,RPL29,RPL32,RPL35,RPL7A,RPL8,
RPLP0,RPLP1,RPS11,RPS14,RPS3,RPS5,RPS8
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 RPL29


There's no related Drug.
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Cross referenced IDs for RPL29
* 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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