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 RPL37
Basic gene info.Gene symbolRPL37
Gene nameribosomal protein L37
SynonymsL37
CytomapUCSC genome browser: 5p13
Genomic locationchr5 :40831429-40835387
Type of geneprotein-coding
RefGenesNM_000997.4,
Ensembl idENSG00000145592
Description60S ribosomal protein L3760S ribosomal protein L37aG1.16
Modification date20141207
dbXrefs MIM : 604181
HGNC : HGNC
HPRD : 16047
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPL37
BioGPS: 6167
Gene Expression Atlas: ENSG00000145592
The Human Protein Atlas: ENSG00000145592
PathwayNCI Pathway Interaction Database: RPL37
KEGG: RPL37
REACTOME: RPL37
ConsensusPathDB
Pathway Commons: RPL37
MetabolismMetaCyc: RPL37
HUMANCyc: RPL37
RegulationEnsembl's Regulation: ENSG00000145592
miRBase: chr5 :40,831,429-40,835,387
TargetScan: NM_000997
cisRED: ENSG00000145592
ContextiHOP: RPL37
cancer metabolism search in PubMed: RPL37
UCL Cancer Institute: RPL37
Assigned class in ccmGDBC

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Phenotypic Information for RPL37(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPL37
Familial Cancer Database: RPL37
* 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: RPL37
MedGen: RPL37 (Human Medical Genetics with Condition)
ClinVar: RPL37
PhenotypeMGI: RPL37 (International Mouse Phenotyping Consortium)
PhenomicDB: RPL37

Mutations for RPL37
* 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 RPL37 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AJ705329MBOAT1118662012493320125119RPL3718037454083255640834357
AW136069RPL37176854083256140832612CFLAR642952201981483201981714
BF003129RPL37128254083255840832628UBR5785708103337293103337786
BF726594RPL37113854083458840835301LOC254100139507116533762265338083

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample        1        
GAIN (# sample)        1        
LOSS (# sample)                 
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=9

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=16)
Stat. for Synonymous SNVs
(# total SNVs=1)
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
chr5:40834367-40834367p.Y47F9
chr5:40834695-40834695p.S6*3
chr5:40834624-40834624p.Q30*2
chr5:40832665-40832665p.R79C1
chr5:40835298-40835298p.?1
chr5:40834286-40834286p.F74S1
chr5:40834293-40834293p.R72C1
chr5:40834304-40834304p.K68I1
chr5:40834599-40834599p.G38D1
chr5:40834616-40834616p.S32S1

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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
# sample1          11   1  2
# mutation1          11   1  2
nonsynonymous SNV1          11      2
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
chr5:40832665p.R79C1
chr5:40834286p.F74S1
chr5:40834293p.R72C1
chr5:40834304p.K68I1
chr5:40834695p.S6L1
chr5:40832606p.X98X1

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 RPL37 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 RPL37

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,RPL13,RPL18,RPL24,RPL27A,RPL28,RPL29,
RPL31,RPL32,RPL35,RPL36,RPL37,RPL37A,RPLP2,
RPS10,RPS11,RPS14,RPS15,RPS19,RPS8,RPS9
PHB2,RPL10,RPL13,RPL14,RPL18,RPL18A,RPL19,
RPL29,RPL32,RPL35,RPL37,RPL37A,RPL4,RPS11,
RPS12,RPS14,RPS16,RPS21,RPS23,RPS6,RPS8

EEF1B2,RPL10A,RPL12,RPL14,RPL29,RPL31,RPL32,
RPL35A,RPL36,RPL37,RPL37A,RPL38,RPL7A,RPS13,
RPS17,RPS18,RPS23,RPS25,RPS27A,RPS6,RPS7
RPL18,RPL18A,RPL19,RPL32,RPL36,RPL37,RPL37A,
RPL38,RPL7A,RPL8,RPLP0,RPLP1,RPS10,RPS12,
RPS16,RPS19,RPS21,RPS23,RPS29,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 RPL37
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 L37experimentalAlpha-Hydroxy-Beta-Phenyl-Propionic Acid
DB04602ribosomal protein L37experimentalPUROMYCIN AMINONUCLEOSIDE-5'-MONOPHOSPHATE
DB04805ribosomal protein L37experimentalVirginiamycin factor S1
DB07374ribosomal protein L37experimentalANISOMYCIN
DB08437ribosomal protein L37experimentalPUROMYCIN


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Cross referenced IDs for RPL37
* 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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