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 RPL31
Basic gene info.Gene symbolRPL31
Gene nameribosomal protein L31
SynonymsL31
CytomapUCSC genome browser: 2q11.2
Genomic locationchr2 :101618690-101636155
Type of geneprotein-coding
RefGenesNM_000993.4,
NM_001098577.2,NM_001099693.1,
Ensembl idENSG00000071082
Description60S ribosomal protein L31
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000071082
HPRD : 17994
Vega : OTTHUMG00000130687
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPL31
BioGPS: 6160
Gene Expression Atlas: ENSG00000071082
The Human Protein Atlas: ENSG00000071082
PathwayNCI Pathway Interaction Database: RPL31
KEGG: RPL31
REACTOME: RPL31
ConsensusPathDB
Pathway Commons: RPL31
MetabolismMetaCyc: RPL31
HUMANCyc: RPL31
RegulationEnsembl's Regulation: ENSG00000071082
miRBase: chr2 :101,618,690-101,636,155
TargetScan: NM_000993
cisRED: ENSG00000071082
ContextiHOP: RPL31
cancer metabolism search in PubMed: RPL31
UCL Cancer Institute: RPL31
Assigned class in ccmGDBC

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Phenotypic Information for RPL31(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPL31
Familial Cancer Database: RPL31
* 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: RPL31
MedGen: RPL31 (Human Medical Genetics with Condition)
ClinVar: RPL31
PhenotypeMGI: RPL31 (International Mouse Phenotyping Consortium)
PhenomicDB: RPL31

Mutations for RPL31
* 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 RPL31 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DB263110RPL311632101618755101619203MYLK-AS1625933123331337123331867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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=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
chr2:101622832-101622832p.D123Y2
chr2:101622468-101622468p.E94V1
chr2:101619172-101619172p.P3P1
chr2:101622473-101622473p.E96K1
chr2:101619195-101619195p.K11R1
chr2:101622476-101622476p.D97N1
chr2:101620636-101620636p.A42T1
chr2:101622534-101622534p.?1
chr2:101620642-101620642p.R44W1
chr2:101622541-101622541p.?1

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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
# sample2  3  1          1  
# mutation4  3  1          1  
nonsynonymous SNV4  3  1          1  
synonymous SNV                    
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
chr2:101620636p.A42T,RPL311
chr2:101620679p.E56G,RPL311
chr2:101622467p.E94K,RPL311
chr2:101622468p.E94V,RPL311
chr2:101622470p.D95N,RPL311
chr2:101622473p.E96K,RPL311
chr2:101622476p.D97N,RPL311
chr2:101622541p.F118L1
chr2:101622832p.D123N1

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 RPL31 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 RPL31

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

RPL10A,RPL11,RPL12,RPL24,RPL27A,RPL29,RPL31,
RPL32,RPL34,RPL35A,RPL36,RPL37,RPL37A,RPL6,
RPL7A,RPS11,RPS14,RPS18,RPS2,RPS8,RPS9
EEF1A1,RPL10,RPL10A,RPL14,RPL23A,RPL31,RPL32,
RPL35A,RPL37,RPL4,RPL5,RPL6,RPS12,RPS14,
RPS23,RPS27A,RPS4X,RPS6,RPS7,RPS8,RPSAP58

RPL10A,RPL12,RPL31,RPL32,RPL34,RPL35A,RPL36,
RPL37,RPL37A,RPL38,RPL7A,RPS11,RPS14,RPS15A,
RPS18,RPS23,RPS25,RPS27A,RPS6,RPS7,RPS8
EEF1A1,RPL10,RPL12,RPL15,RPL17,RPL19,RPL30,
RPL31,RPL32,RPL35A,RPL38,RPL41,RPL5,RPL6,
RPL7A,RPS12,RPS13,RPS20,RPS23,RPS24,RPS25
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 RPL31


There's no related Drug.
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Cross referenced IDs for RPL31
* 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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