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 GRPEL2
Basic gene info.Gene symbolGRPEL2
Gene nameGrpE-like 2, mitochondrial (E. coli)
SynonymsMt-GrpE#2
CytomapUCSC genome browser: 5q32
Genomic locationchr5 :148724976-148734146
Type of geneprotein-coding
RefGenesNM_152407.3,
Ensembl idENSG00000164284
DescriptiongrpE protein homolog 2, mitochondrial
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000164284
HPRD : 17079
Vega : OTTHUMG00000130048
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GRPEL2
BioGPS: 134266
Gene Expression Atlas: ENSG00000164284
The Human Protein Atlas: ENSG00000164284
PathwayNCI Pathway Interaction Database: GRPEL2
KEGG: GRPEL2
REACTOME: GRPEL2
ConsensusPathDB
Pathway Commons: GRPEL2
MetabolismMetaCyc: GRPEL2
HUMANCyc: GRPEL2
RegulationEnsembl's Regulation: ENSG00000164284
miRBase: chr5 :148,724,976-148,734,146
TargetScan: NM_152407
cisRED: ENSG00000164284
ContextiHOP: GRPEL2
cancer metabolism search in PubMed: GRPEL2
UCL Cancer Institute: GRPEL2
Assigned class in ccmGDBC

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Phenotypic Information for GRPEL2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GRPEL2
Familial Cancer Database: GRPEL2
* 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

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GRPEL2
MedGen: GRPEL2 (Human Medical Genetics with Condition)
ClinVar: GRPEL2
PhenotypeMGI: GRPEL2 (International Mouse Phenotyping Consortium)
PhenomicDB: GRPEL2

Mutations for GRPEL2
* 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 GRPEL2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
N40724GRPEL212915148733379148733669GRPEL22824295148733855148734002

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=13)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=0)
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
chr5:148730671-148730671p.P168P2
chr5:148730567-148730567p.E134K2
chr5:148730799-148730817p.L212fs*>81
chr5:148727914-148727914p.L53F1
chr5:148730653-148730653p.G162G1
chr5:148730806-148730806p.A213A1
chr5:148727935-148727935p.R60*1
chr5:148730657-148730657p.E164*1
chr5:148730818-148730818p.V217V1
chr5:148727972-148727972p.E72V1

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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
# sample11 2     1 112  1  2
# mutation11 2     1 112  1  2
nonsynonymous SNV11          12  1  1
synonymous SNV   2     1 1       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
chr5:148727972p.E72V1
chr5:148730622p.A152V1
chr5:148730653p.G162G1
chr5:148730659p.E164E1
chr5:148730726p.G187C1
chr5:148730727p.G187V1
chr5:148730749p.T194T1
chr5:148730750p.V195M1
chr5:148727842p.A196A1
chr5:148730755p.G207S1

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 GRPEL2 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 GRPEL2

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

ANKHD1,SPDL1,CDC23,ETF1,G3BP1,GRPEL2,HMMR,
HSPA9,LARP1,LARS,NPM1,RARS,RBM22,RBM27,
SRSF10,SRSF1,SMAD5,TCERG1,UBE2D2,ZFP62,ZNF354A
C14orf28,C3orf38,C6orf62,RBM48,CCDC117,CGGBP1,GRPEL2,
MSANTD4,NANP,NSL1,RNF219,SREK1IP1,TAF9B,TBL1XR1,
THAP1,TRIM13,ZBTB34,ZBTB6,ZBTB14,ZNF566,ZNF684

PARPBP,CCDC59,CCNB1,CCNH,CCT2,CDK1,CENPK,
GRPEL2,HINT1,MAD2L1,MRPL22,MRPL42,MRPS27,NPM1,
PPP2CA,RIOK2,SREK1IP1,TAF9,TBCA,UBE2N,ZCCHC9
ARL5A,ATG3,BET1,BUD13,CBX3,PBDC1,ENOPH1,
FOXN2,GLO1,GRPEL2,LSM6,OSTC,PEX3,TRMT10A,
RIOK2,SEC22B,SMS,SVIP,UCHL5,ZC3H15,ZCCHC9
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 GRPEL2


There's no related Drug.
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Cross referenced IDs for GRPEL2
* 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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