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 PLTP
Basic gene info.Gene symbolPLTP
Gene namephospholipid transfer protein
SynonymsBPIFE|HDLCQ9
CytomapUCSC genome browser: 20q13.12
Genomic locationchr20 :44527258-44541003
Type of geneprotein-coding
RefGenesNM_001242920.1,
NM_001242921.1,NM_006227.3,NM_182676.2,
Ensembl idENSG00000100979
DescriptionBPI fold containing family Elipid transfer protein II
Modification date20141207
dbXrefs MIM : 172425
HGNC : HGNC
Ensembl : ENSG00000100979
HPRD : 01399
Vega : OTTHUMG00000033047
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PLTP
BioGPS: 5360
Gene Expression Atlas: ENSG00000100979
The Human Protein Atlas: ENSG00000100979
PathwayNCI Pathway Interaction Database: PLTP
KEGG: PLTP
REACTOME: PLTP
ConsensusPathDB
Pathway Commons: PLTP
MetabolismMetaCyc: PLTP
HUMANCyc: PLTP
RegulationEnsembl's Regulation: ENSG00000100979
miRBase: chr20 :44,527,258-44,541,003
TargetScan: NM_001242920
cisRED: ENSG00000100979
ContextiHOP: PLTP
cancer metabolism search in PubMed: PLTP
UCL Cancer Institute: PLTP
Assigned class in ccmGDBC

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

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

Mutations for PLTP
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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
breastPLTPchr204453411144534111chr204457698044576980
pancreasPLTPchr204453536144535381PLTPchr204453577444535794
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 PLTP 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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=46)
Stat. for Synonymous SNVs
(# total SNVs=13)
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
chr20:44530927-44530927p.R385L3
chr20:44540080-44540080p.F4F2
chr20:44533618-44533618p.R282Q2
chr20:44528489-44528489p.L402M1
chr20:44538160-44538160p.T160T1
chr20:44538612-44538612p.R100S1
chr20:44533495-44533495p.P296T1
chr20:44540031-44540031p.G21C1
chr20:44527588-44527588p.A492T1
chr20:44534909-44534909p.R235W1

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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 81   31 7311 14 7
# mutation11 111   31 7311 15 7
nonsynonymous SNV11 101   2  52 1 14 7
synonymous SNV   1    11 211   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
chr20:44540080p.F4F,PLTP2
chr20:44531163p.F22F,PLTP1
chr20:44534935p.R187W,PLTP1
chr20:44527588p.R12S,PLTP1
chr20:44538612p.A397T,PLTP1
chr20:44533495p.P160T,PLTP1
chr20:44534981p.S8Y,PLTP1
chr20:44527599p.P393L,PLTP1
chr20:44538623p.A157T,PLTP1
chr20:44533604p.E87G,PLTP1

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 PLTP 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 PLTP

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

MILR1,CD248,COL6A2,DAZL,DEFB124,FOLR2,GP9,
LAMC3,LCE3C,LCE3D,LCNL1,MMP9,LINC00162,PCOLCE,
PLTP,PTGDS,RCN3,SPON2,SPRR2G,STAB1,XPNPEP2
C1QA,C1QB,C1QC,C2,CD14,CD163,CD209,
CLEC10A,CRYBB1,CSF1R,FOLR2,LGMN,LILRB2,LILRB5,
MCOLN1,PLTP,RASGRP4,RNASE1,SIGLEC1,STAB1,VSIG4

CTNNBL1,DDX27,DGAT2,FAM117A,FBXO17,LOC644538,LRRC29,
MAMSTR,LINC00086,PAPLN,PLTP,PTPN1,RAB3IL1,RGN,
SMO,SNTA1,SNX21,TSPY26P,TTC7B,TTPAL,USP27X
AQPEP,C4A,CHI3L1,CLDN11,CNBD1,CPXM1,DEFB124,
DYDC1,FAM20A,GLYCAM1,GREM1,LIM2,LOC55908,MARCO,
OR3A4P,PLTP,REG1A,REG1B,RNASE2,SCN1B,SNORA22,
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 PLTP


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