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 RPL38
Basic gene info.Gene symbolRPL38
Gene nameribosomal protein L38
SynonymsL38
CytomapUCSC genome browser: 17q25.1
Genomic locationchr17 :72199794-72206019
Type of geneprotein-coding
RefGenesNM_000999.3,
NM_001035258.1,
Ensembl idENSG00000172809
Description60S ribosomal protein L38
Modification date20141207
dbXrefs MIM : 604182
HGNC : HGNC
Ensembl : ENSG00000172809
HPRD : 16048
Vega : OTTHUMG00000166016
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPL38
BioGPS: 6169
Gene Expression Atlas: ENSG00000172809
The Human Protein Atlas: ENSG00000172809
PathwayNCI Pathway Interaction Database: RPL38
KEGG: RPL38
REACTOME: RPL38
ConsensusPathDB
Pathway Commons: RPL38
MetabolismMetaCyc: RPL38
HUMANCyc: RPL38
RegulationEnsembl's Regulation: ENSG00000172809
miRBase: chr17 :72,199,794-72,206,019
TargetScan: NM_000999
cisRED: ENSG00000172809
ContextiHOP: RPL38
cancer metabolism search in PubMed: RPL38
UCL Cancer Institute: RPL38
Assigned class in ccmGDBC

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Phenotypic Information for RPL38(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPL38
Familial Cancer Database: RPL38
* 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: RPL38
MedGen: RPL38 (Human Medical Genetics with Condition)
ClinVar: RPL38
PhenotypeMGI: RPL38 (International Mouse Phenotyping Consortium)
PhenomicDB: RPL38

Mutations for RPL38
* 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 RPL38 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CK004088NDRG23462142148616121488735RPL38448599177220028872205435
BX101889TEK162392717322427190586RPL38617743177220532572205450
BE388615RPL381291177220005672206007CITED1292494X7152648971526691
BE409397RPL381291177220005672206007CITED1292664X7152596871526691
R50162RPL381205177220532572206054TEK19933392718555427190586
AK075017UBE2J221674111898571209212RPL3816721747177220594272206017
AV742653PRR1343172125383648253837268RPL38163508177219982672206015
BE391347RPL3819300177220006772206007CITED1301555X7152644171526691
BE797621RPL3823527177219984372206008DONSON521837213527624735281514
CA313275MNT181591722873672287508RPL38152496177219981872205995
BP222381RPL381274177219981172205423PHF20269581203435994634450996
BF696633RPL38245177219984372199886SNX3436146108532890108533458
CD368190RPL3817208177220533472206019RPL3203697223971018139712824
CA432338RPL381769177220596772206019TRMT561743146144220461444273
BI861689SUPT7L144622787637927878441RPL38440521177220007772200329
DA794650RPL381295177219981772205450HSP90AA129650114102552631102553443
BM968470RPL381763177220597372206019RPL3859258177220532672206019
AA034452PXN112712120655334120655460RPL38116246177220539472206019
AA017134RPL38254177220596772206019DST4932865632842556330941
CR746137SURF6192489136199133136199561RPL38233599177219981772206016
BM810069RPL3833437177219995472206019NCAPH2438961225096235250962869
DB371044RPL38176177220594272206017UBE2J274504111898571190295
AA977713RPL382277177220596372206019TRAPPC6B64423143961932939619688
BC046153PMS2P31394277514401175157428RPL389321003177220594872206019

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=1

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=1)
Stat. for Synonymous SNVs
(# total SNVs=3)
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
chr17:72205348-72205348p.K29K1
chr17:72205355-72205355p.V32M1
chr17:72205370-72205370p.R37*1
chr17:72205441-72205442p.G63fs*>91
chr17:72205447-72205447p.P62P1
chr17:72205953-72205953p.V66V1

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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   2             1  
# mutation   2             1  
nonsynonymous SNV                 1  
synonymous SNV   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
chr17:72205348p.V32M,RPL381
chr17:72205355p.V66V,RPL381
chr17:72205953p.K29K,RPL381

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 RPL38 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 RPL38

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

C17orf89,FAU,MRPL12,MRPL38,NAT9,RPL13,RPL18,
RPL24,RPL27A,RPL32,RPL35,RPL36,RPL37,RPL37A,
RPL38,RPL39,RPLP2,RPS19,RPS2,SNRPA,SNRPD2
EIF3F,MRPL9,RPL11,RPL24,RPL27,RPL27A,RPL30,
RPL32,RPL35A,RPL37,RPL38,RPL41,RPL6,RPS11,
RPS15A,RPS17,RPS23,RPS24,RPS25,RPS29,RPS7

NME2,RPL12,RPL23A,RPL24,RPL27,RPL29,RPL31,
RPL32,RPL35,RPL35A,RPL36,RPL37A,RPL38,RPL7A,
RPLP2,RPS10,RPS13,RPS16,RPS25,RPS3,RPS9
EEF1A1,RPL10,RPL14,RPL15,RPL19,RPL30,RPL32,
RPL35A,RPL37A,RPL38,RPL7A,RPLP1,RPS10,RPS11,
RPS12,RPS13,RPS16,RPS23,RPS25,RPS3,RPS9
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 RPL38


There's no related Drug.
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Cross referenced IDs for RPL38
* 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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