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 RPL3
Basic gene info.Gene symbolRPL3
Gene nameribosomal protein L3
SynonymsASC-1|L3|TARBP-B
CytomapUCSC genome browser: 22q13
Genomic locationchr22 :39708886-39715670
Type of geneprotein-coding
RefGenesNM_000967.3,
NM_001033853.1,
Ensembl idENSG00000100316
Description60S ribosomal protein L3HIV-1 TAR RNA-binding protein Bhypothetical protein
Modification date20141207
dbXrefs MIM : 604163
HGNC : HGNC
Ensembl : ENSG00000100316
HPRD : 16042
Vega : OTTHUMG00000151079
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPL3
BioGPS: 6122
Gene Expression Atlas: ENSG00000100316
The Human Protein Atlas: ENSG00000100316
PathwayNCI Pathway Interaction Database: RPL3
KEGG: RPL3
REACTOME: RPL3
ConsensusPathDB
Pathway Commons: RPL3
MetabolismMetaCyc: RPL3
HUMANCyc: RPL3
RegulationEnsembl's Regulation: ENSG00000100316
miRBase: chr22 :39,708,886-39,715,670
TargetScan: NM_000967
cisRED: ENSG00000100316
ContextiHOP: RPL3
cancer metabolism search in PubMed: RPL3
UCL Cancer Institute: RPL3
Assigned class in ccmGDBC

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Phenotypic Information for RPL3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPL3
Familial Cancer Database: RPL3
* 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: RPL3
MedGen: RPL3 (Human Medical Genetics with Condition)
ClinVar: RPL3
PhenotypeMGI: RPL3 (International Mouse Phenotyping Consortium)
PhenomicDB: RPL3

Mutations for RPL3
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows RPL3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CN268128EMILIN1114522730158927301733RPL3141193223970888939708941
BQ349966RPL310328223971353939715630RPL3323592223971019839711466
BQ923637HLA-B148625815232581571RPL345813223971069939714528
CD699756LPAR5422101267306036745126RPL3201606223971143439713608
AL702234SEPT1115447794983077949883RPL348163223970889439709215
CV360980MICB22334625949122596137RPL3331584223971069139711466
BP429026GPX1729234939492549395489RPL3291388223970970339710177
BG505035FLT3LG2522194999086549994778RPL3521637223970891539709232
BM972994PPAPDC1B1754583812450038125533RPL3539689223971359839714519
AA242792RPL31154223971137339711526SOX81544901610364431036779
CD368190RPL3817208177220533472206019RPL3203697223971018139712824
CX786698RPL31495223971142939714462BCL2L2-PABPN1491616142379515323795279
AW999090NGLY11528332577384825775506RPL3269539223971305839713328
BF360749RPL361213223971069139710841STX112022226144483951144483971

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=19)
Stat. for Synonymous SNVs
(# total SNVs=10)
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
chr22:39713525-39713525p.F102F2
chr22:39714490-39714490p.P37P2
chr22:39712827-39712827p.A129T1
chr22:39710171-39710171p.L298M1
chr22:39711490-39711490p.A191D1
chr22:39712841-39712841p.K124T1
chr22:39710186-39710186p.I293F1
chr22:39711492-39711492p.V190V1
chr22:39708972-39708972p.D395E1
chr22:39710189-39710189p.L292F1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample31 7    41 31   42 4
# mutation31 7    41 31   42 4
nonsynonymous SNV1  6    21 1    22 2
synonymous SNV21 1    2  21   2  2
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
chr22:39713525p.F102F,RPL32
chr22:39710719p.R261H,RPL31
chr22:39712790p.K39N,RPL31
chr22:39710727p.I220I,RPL31
chr22:39712805p.P206P,RPL31
chr22:39708972p.V190V,RPL31
chr22:39710735p.D395E,RPL31
chr22:39712807p.L180L,RPL31
chr22:39708981p.L392L,RPL31
chr22:39710758p.P172T1

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 RPL3 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 RPL3

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

C1QTNF9B,CT45A1,CT45A3,DHRS2,FRG2B,GABPB1,HGC6.3,
LOC643008,MAGEA8,MAGEB18,MAGEB2,RGS5,RPL3L,SPPL2A,
SUMO2,TYRP1,UGT2B10,UGT2B15,USP29,USP8,ZIM3
ACTA1,ATP2A1,MIR1-1HG,CKM,CSRP3,LMOD2,LOC151300,
MYBPC2,MYH2,MYH6,MYH7,MYL1,MYL2,MYLPF,
NEB,NRAP,OR5H15,P2RX6P,PPP1R3A,RPL3L,XIRP2

PPP1R17,LINC00588,CACNG7,CER1,CHRNA4,CPLX3,FAM27L,
LHX3,PAQR9,RBMY1A3P,RPL3L,SHISA7,SLC1A6,SLC6A5,
TFAP2D,TSPY1,TSPY4,UNCX
ACTBL2,LINC00596,SCP2D1,DUOX1,FAM74A1,FAM92A1P2,FLJ25758,
GAL,HELT,KRTAP13-1,LY6D,MCHR1,OR1J2,PFN3,
PRAMEF12,RBMXL3,RPL3L,SNORA64,SNORA74A,tAKR,TM4SF19,
TRIM42,USP26,VWCE,X
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 RPL3
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
DB02494ribosomal protein L3experimentalAlpha-Hydroxy-Beta-Phenyl-Propionic Acid
DB07374ribosomal protein L3experimentalANISOMYCIN
DB08437ribosomal protein L3experimentalPUROMYCIN


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Cross referenced IDs for RPL3
* 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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