Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 LONP2
Basic gene info.Gene symbolLONP2
Gene namelon peptidase 2, peroxisomal
SynonymsLONP|LONPL
CytomapUCSC genome browser: 16q12.1
Genomic locationchr16 :48278210-48387407
Type of geneprotein-coding
RefGenesNM_001300948.1,
NM_031490.3,
Ensembl idENSG00000102910
Descriptionlon protease 2lon protease homolog 2, peroxisomallon protease-like protein 2peroxisomal LON protease likeperoxisomal Lon protease homolog 2
Modification date20141207
dbXrefs HGNC : HGNC
HPRD : 07491
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LONP2
BioGPS: 83752
Gene Expression Atlas: ENSG00000102910
The Human Protein Atlas: ENSG00000102910
PathwayNCI Pathway Interaction Database: LONP2
KEGG: LONP2
REACTOME: LONP2
ConsensusPathDB
Pathway Commons: LONP2
MetabolismMetaCyc: LONP2
HUMANCyc: LONP2
RegulationEnsembl's Regulation: ENSG00000102910
miRBase: chr16 :48,278,210-48,387,407
TargetScan: NM_001300948
cisRED: ENSG00000102910
ContextiHOP: LONP2
cancer metabolism search in PubMed: LONP2
UCL Cancer Institute: LONP2
Assigned class in ccmGDBC

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Phenotypic Information for LONP2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: LONP2
Familial Cancer Database: LONP2
* 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: LONP2
MedGen: LONP2 (Human Medical Genetics with Condition)
ClinVar: LONP2
PhenotypeMGI: LONP2 (International Mouse Phenotyping Consortium)
PhenomicDB: LONP2

Mutations for LONP2
* 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 LONP2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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=55)
Stat. for Synonymous SNVs
(# total SNVs=12)
Stat. for Deletions
(# total SNVs=1)
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
chr16:48381506-48381506p.R676Q2
chr16:48385596-48385596p.N814N2
chr16:48278396-48278396p.V33L2
chr16:48290555-48290555p.V168D2
chr16:48329968-48329968p.L476L2
chr16:48295386-48295391p.E265_D266delED1
chr16:48311243-48311243p.?1
chr16:48385508-48385508p.D785G1
chr16:48296726-48296726p.L309V1
chr16:48330057-48330057p.M505I1

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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
# sample54 81 4 51 54   8919
# mutation54 81 4 51 84   9919
nonsynonymous SNV13 61 3 4  74   7716
synonymous SNV41 2  1 11 1    22 3
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
chr16:48381506p.R676Q2
chr16:48385596p.R246H2
chr16:48295348p.N814N2
chr16:48303932p.E829D1
chr16:48381495p.L101L1
chr16:48304164p.P321S1
chr16:48385510p.L440V1
chr16:48290626p.V647A1
chr16:48337093p.F108L1
chr16:48303939p.L330V1

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 LONP2 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 LONP2

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

ABCC11,ADAT1,AP1G1,DNAJA2,EARS2,GLUD2,GSPT1,
HEATR3,ITFG1,LONP2,N4BP1,PAPD5,PDP2,PDPK1,
PHKB,RBL2,RPGRIP1L,RSPRY1,SIAH1,CNEP1R1,VPS35
ABCC11,ACSL3,ADAM2,ALOX15B,B3GAT1,BRI3BP,C6orf223,
DHRS2,HMGCS1,HPGD,IDI1,LONP2,MPV17L,PNLIPRP3,
SERHL2,SERHL,SRD5A1,TARP,TMPRSS11F,UGT2B10,UGT2B28

ADAT1,AP1G1,ATXN1L,MAB21L3,CNOT1,GSPT1,HEATR3,
ITFG1,LMBRD2,LONP2,MON1B,N4BP1,PAPD5,PDP2,
PHKB,RBL2,RSC1A1,RSPRY1,SIAH1,USP10,VPS35
ACO1,AHCYL1,ATF6,NRDE2,CREB3L2,DDB1,EPRS,
EXOC6B,GGCX,GIGYF2,GLG1,GNS,GSK3B,ICMT,
LONP2,NBAS,NFATC3,PIK3R4,RBM27,SMARCA5,SMC3
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 LONP2


There's no related Drug.
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Cross referenced IDs for LONP2
* 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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