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 LYPLA1
Basic gene info.Gene symbolLYPLA1
Gene namelysophospholipase I
SynonymsAPT-1|APT1|LPL-I|LPL1|hAPT1
CytomapUCSC genome browser: 8q11.23
Genomic locationchr8 :54958937-55014577
Type of geneprotein-coding
RefGenesNM_001279356.1,
NM_001279357.1,NM_001279358.1,NM_001279359.1,NM_001279360.1,
NM_006330.3,
Ensembl idENSG00000120992
Descriptionacyl-protein thioesterase 1lysoPLA Ilysophospholipid-specific lysophospholipase
Modification date20141207
dbXrefs MIM : 605599
HGNC : HGNC
Ensembl : ENSG00000120992
HPRD : 07063
Vega : OTTHUMG00000164313
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LYPLA1
BioGPS: 10434
Gene Expression Atlas: ENSG00000120992
The Human Protein Atlas: ENSG00000120992
PathwayNCI Pathway Interaction Database: LYPLA1
KEGG: LYPLA1
REACTOME: LYPLA1
ConsensusPathDB
Pathway Commons: LYPLA1
MetabolismMetaCyc: LYPLA1
HUMANCyc: LYPLA1
RegulationEnsembl's Regulation: ENSG00000120992
miRBase: chr8 :54,958,937-55,014,577
TargetScan: NM_001279356
cisRED: ENSG00000120992
ContextiHOP: LYPLA1
cancer metabolism search in PubMed: LYPLA1
UCL Cancer Institute: LYPLA1
Assigned class in ccmGDBC

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Phenotypic Information for LYPLA1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: LYPLA1
Familial Cancer Database: LYPLA1
* 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: LYPLA1
MedGen: LYPLA1 (Human Medical Genetics with Condition)
ClinVar: LYPLA1
PhenotypeMGI: LYPLA1 (International Mouse Phenotyping Consortium)
PhenomicDB: LYPLA1

Mutations for LYPLA1
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
prostateLYPLA1chr85500802055008020chr85536753655367536
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows LYPLA1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AK296257SSSCA11640116533794865339230LYPLA1641163185496035855014414
DB459081LYPLA1127085501346855014552PFKP2703701031544773154577

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     2 2     1
GAIN (# sample)  1     2 2     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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=14)
Stat. for Synonymous SNVs
(# total SNVs=2)
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
chr8:54963582-54963582p.S210L3
chr8:54978328-54978328p.I49M2
chr8:54965242-54965242p.W145C2
chr8:54963657-54963657p.T185M1
chr8:54963679-54963679p.P178S1
chr8:54978369-54978369p.G36R1
chr8:54963680-54963680p.V177V1
chr8:54965251-54965251p.L142L1
chr8:54965265-54965265p.G138S1
chr8:54965303-54965303p.S125Y1

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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
# sample1  1    1  131  21 1
# mutation1  1    1  131  21 1
nonsynonymous SNV        1  13   1  1
synonymous SNV1  1         1  11  
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
chr8:54963656p.S176L,LYPLA12
chr8:54963582p.T151T,LYPLA12
chr8:54963680p.G100R,LYPLA11
chr8:54965251p.N95K,LYPLA11
chr8:54965265p.D69D,LYPLA11
chr8:54967634p.G36R,LYPLA11
chr8:54967647p.P161L,LYPLA11
chr8:54974845p.V152V,LYPLA11
chr8:54978369p.V143V,LYPLA11
chr8:54963627p.L126L,LYPLA11

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 LYPLA1 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 LYPLA1

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

ARFGEF1,ARMC1,ATP6V1C1,ATP6V1H,AZIN1,CPNE3,DPY19L4,
IMPAD1,LYPLA1,MTFR1,PEX2,RAB2A,RB1CC1,STAU2,
TCEA1,TMEM68,TRAM1,UBE2W,VCPIP1,WWP1,YTHDF3
AP1AR,BUB3,C5orf22,SMIM15,TRAPPC13,MICU2,GPR160,
GZF1,LYPLA1,MOB4,MRPL42,NDFIP2,PGGT1B,RAD1,
RNF2,SCOC,SLC30A9,SLMO2,TMEM33,TRUB1,UBE2K

ARMC1,C12orf29,NDUFAF6,C8orf76,CAPZA2,COMMD8,COPS5,
CPNE3,LYPLA1,MRPL13,MRPL15,MTFR1,NSMCE2,NUDCD1,
PEX2,SEP15,SLC25A32,TMEM68,TMEM70,UBE2W,YTHDF3
ATG5,ATP5O,DTD2,TEFM,CCNC,CNIH1,COMMD8,
LYPLA1,MRPL13,MRPL15,MRPL32,MRPL49,NDUFB5,NIPSNAP3A,
PEX2,SELT,SEP15,TMEM14B,TMEM183A,WDR61,YEATS4
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 LYPLA1
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
DB00360lysophospholipase Iapproved; investigationalTetrahydrobiopterin


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Cross referenced IDs for LYPLA1
* 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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