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 LYPLA2
Basic gene info.Gene symbolLYPLA2
Gene namelysophospholipase II
SynonymsAPT-2|DJ886K2.4
CytomapUCSC genome browser: 1p36.11
Genomic locationchr1 :24117645-24122029
Type of geneprotein-coding
RefGenesNM_007260.2,
Ensembl idENSG00000011009
DescriptionLPL-IIacyl-protein thioesterase 2lysoPLA II
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000011009
HPRD : 07127
Vega : OTTHUMG00000002961
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LYPLA2
BioGPS: 11313
Gene Expression Atlas: ENSG00000011009
The Human Protein Atlas: ENSG00000011009
PathwayNCI Pathway Interaction Database: LYPLA2
KEGG: LYPLA2
REACTOME: LYPLA2
ConsensusPathDB
Pathway Commons: LYPLA2
MetabolismMetaCyc: LYPLA2
HUMANCyc: LYPLA2
RegulationEnsembl's Regulation: ENSG00000011009
miRBase: chr1 :24,117,645-24,122,029
TargetScan: NM_007260
cisRED: ENSG00000011009
ContextiHOP: LYPLA2
cancer metabolism search in PubMed: LYPLA2
UCL Cancer Institute: LYPLA2
Assigned class in ccmGDBC

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Phenotypic Information for LYPLA2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: LYPLA2
Familial Cancer Database: LYPLA2
* 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
KEGG_GLYCEROPHOSPHOLIPID_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: LYPLA2
MedGen: LYPLA2 (Human Medical Genetics with Condition)
ClinVar: LYPLA2
PhenotypeMGI: LYPLA2 (International Mouse Phenotyping Consortium)
PhenomicDB: LYPLA2

Mutations for LYPLA2
* 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 LYPLA2 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=11)
Stat. for Synonymous SNVs
(# total SNVs=4)
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
chr1:24120404-24120404p.K93N2
chr1:24121190-24121190p.E222*2
chr1:24121199-24121199p.E225Q2
chr1:24120961-24120961p.H172H2
chr1:24119706-24119706p.A59V1
chr1:24121071-24121071p.M209T1
chr1:24120212-24120212p.T65I1
chr1:24121077-24121077p.S211I1
chr1:24120368-24120368p.L81L1
chr1:24121170-24121172p.?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
# sample   2       2 1  3  6
# mutation   2       2 1  3  6
nonsynonymous SNV   1       1 1  1  6
synonymous SNV   1       1    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
chr1:24120404p.I103N1
chr1:24120565p.G110W1
chr1:24120585p.P112S1
chr1:24120591p.L133I1
chr1:24120741p.P180P1
chr1:24120985p.V195V1
chr1:24121030p.P197L1
chr1:24121035p.M209T1
chr1:24119680p.S211I1
chr1:24121071p.E222K1

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 LYPLA2 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 LYPLA2

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

AGTRAP,AURKAIP1,C1orf86,C9orf16,CDC34,CPTP,GPATCH3,
GUK1,LYPLA2,LYPLA2P1,MIIP,NUDC,PQLC2,PUSL1,
SURF2,THAP3,UBE2J2,ZBTB17,ZFAND2B,ZNF593,ZNHIT1
AGTRAP,ARF5,B3GAT3,R3HDM4,EMC10,C9orf142,CHPF,
HSPBP1,LYPLA2,MFSD10,OTUB1,PAFAH1B3,PPP1CA,PPP4C,
PUSL1,SIRT6,TARBP2,TMEM134,TRIM28,WDR34,YIPF2

ATP13A2,ATPIF1,TSR3,PITHD1,MINOS1,CNKSR1,DGAT1,
GALE,CPTP,HMGCL,KIAA2013,LYPLA2,LYPLA2P1,NUDC,
PEX14,PQLC2,RPS6KA1,SLC22A18,STUB1,TIAF1,TMEM222
APEX2,ARHGDIA,ATP6V0D1,ATXN7L3,BAX,BRMS1,CFL1,
CLTB,DOK4,ELOVL1,GNB2,HN1,KRT18,KRT8,
LYPLA2,PKP3,SH3BGRL3,SIRT6,STXBP2,TMEM53,TSPAN1
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 LYPLA2


There's no related Drug.
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Cross referenced IDs for LYPLA2
* 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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