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 LAP3
Basic gene info.Gene symbolLAP3
Gene nameleucine aminopeptidase 3
SynonymsHEL-S-106|LAP|LAPEP|PEPS
CytomapUCSC genome browser: 4p15.32
Genomic locationchr4 :17578926-17609590
Type of geneprotein-coding
RefGenesNM_015907.2,
Ensembl idENSG00000002549
DescriptionLAP-3cytosol aminopeptidaseepididymis secretory protein Li 106leucyl aminopeptidasepeptidase Sproline aminopeptidaseprolyl aminopeptidase
Modification date20141222
dbXrefs MIM : 170250
HGNC : HGNC
Ensembl : ENSG00000002549
HPRD : 07516
Vega : OTTHUMG00000048214
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LAP3
BioGPS: 51056
Gene Expression Atlas: ENSG00000002549
The Human Protein Atlas: ENSG00000002549
PathwayNCI Pathway Interaction Database: LAP3
KEGG: LAP3
REACTOME: LAP3
ConsensusPathDB
Pathway Commons: LAP3
MetabolismMetaCyc: LAP3
HUMANCyc: LAP3
RegulationEnsembl's Regulation: ENSG00000002549
miRBase: chr4 :17,578,926-17,609,590
TargetScan: NM_015907
cisRED: ENSG00000002549
ContextiHOP: LAP3
cancer metabolism search in PubMed: LAP3
UCL Cancer Institute: LAP3
Assigned class in ccmGDBC

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Phenotypic Information for LAP3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: LAP3
Familial Cancer Database: LAP3
* 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_ARGININE_AND_PROLINE_METABOLISM
KEGG_GLUTATHIONE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: LAP3
MedGen: LAP3 (Human Medical Genetics with Condition)
ClinVar: LAP3
PhenotypeMGI: LAP3 (International Mouse Phenotyping Consortium)
PhenomicDB: LAP3

Mutations for LAP3
* 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 LAP3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG566103LAP3146341757912017585220SERPINA1458778149484471094845846
CV416019LAP319941760737717607475REPS298123X1706237517062401
BF377094LAP3626941759608917596353LAP326134641759579517595880

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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=38)
Stat. for Synonymous SNVs
(# total SNVs=15)
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
chr4:17609065-17609065p.F471F4
chr4:17609072-17609072p.H474Y3
chr4:17586688-17586688p.T211T3
chr4:17581474-17581474p.E44*3
chr4:17586653-17586653p.R200C2
chr4:17590506-17590506p.E257*2
chr4:17600150-17600150p.P383P2
chr4:17590484-17590484p.L249L1
chr4:17579091-17579091p.M1I1
chr4:17598694-17598694p.M338I1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample12 6  2 11 73 1 14 9
# mutation12 7  2 11 83 1 14 11
nonsynonymous SNV11 4  1 11 41    1 9
synonymous SNV 1 3  1    42 1 13 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
chr4:17609065p.F471F3
chr4:17600150p.P383P2
chr4:17606287p.T211T1
chr4:17579127p.F419F1
chr4:17585155p.V13V1
chr4:17590497p.R214K1
chr4:17608497p.E436K1
chr4:17579162p.R25L1
chr4:17585168p.L223H1
chr4:17590506p.E44K1

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 LAP3 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 LAP3

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

APOL3,APOL6,CCR5,CD274,CXCR2P1,EPSTI1,ETV7,
GBP1,GBP5,IFIH1,IRF1,LAP3,LOC400759,NLRC5,
PARP14,PDCD1LG2,SAMHD1,STAT1,TAP1,TAP2,TRIM22
APOL1,ATP1B3,B2M,CMPK2,EPSTI1,GIMAP4,GPR85,
IFI27,IFIT3,IFITM1,IFNAR2,IGFBP7,IL3RA,LAP3,
MX2,PARP9,PLSCR1,PSMB9,RSAD2,STAT1,WARS

APOBEC3G,APOL3,CD74,CTSW,GBP1,GBP4,HLA-DPA1,
HLA-DRA,IFIT3,IRF1,JAK2,LAP3,LOC400759,PARP14,
PARP9,STAT1,TAP1,TYMP,UBD,UBE2L6,WARS
APOL1,CXCL9,CXorf49B,FAM26F,FAM66D,GBP4,GBP7,
GZMA,HRASLS2,IFITM1,SPPL2C,LALBA,LAP3,NUB1,
OR2G2,PADI6,PSME2,SNORA26,STAT1,TAP2,TYMP
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 LAP3


There's no related Drug.
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Cross referenced IDs for LAP3
* 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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