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 PNLIPRP1
Basic gene info.Gene symbolPNLIPRP1
Gene namepancreatic lipase-related protein 1
SynonymsPLRP1
CytomapUCSC genome browser: 10q25.3
Genomic locationchr10 :118350489-118368686
Type of geneprotein-coding
RefGenesNM_001303135.1,
NM_006229.3,
Ensembl idENSG00000262273
Descriptioninactive pancreatic lipase-related protein 1
Modification date20141220
dbXrefs MIM : 604422
HGNC : HGNC
Ensembl : ENSG00000187021
HPRD : 05109
Vega : OTTHUMG00000019109
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PNLIPRP1
BioGPS: 5407
Gene Expression Atlas: ENSG00000262273
The Human Protein Atlas: ENSG00000262273
PathwayNCI Pathway Interaction Database: PNLIPRP1
KEGG: PNLIPRP1
REACTOME: PNLIPRP1
ConsensusPathDB
Pathway Commons: PNLIPRP1
MetabolismMetaCyc: PNLIPRP1
HUMANCyc: PNLIPRP1
RegulationEnsembl's Regulation: ENSG00000262273
miRBase: chr10 :118,350,489-118,368,686
TargetScan: NM_001303135
cisRED: ENSG00000262273
ContextiHOP: PNLIPRP1
cancer metabolism search in PubMed: PNLIPRP1
UCL Cancer Institute: PNLIPRP1
Assigned class in ccmGDBC

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Phenotypic Information for PNLIPRP1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PNLIPRP1
Familial Cancer Database: PNLIPRP1
* 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_GLYCEROLIPID_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PNLIPRP1
MedGen: PNLIPRP1 (Human Medical Genetics with Condition)
ClinVar: PNLIPRP1
PhenotypeMGI: PNLIPRP1 (International Mouse Phenotyping Consortium)
PhenomicDB: PNLIPRP1

Mutations for PNLIPRP1
* 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
ovaryPNLIPRP1chr10118368476118368496chr10118369355118369375
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 PNLIPRP1 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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=66)
Stat. for Synonymous SNVs
(# total SNVs=20)
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
chr10:118357393-118357393p.D210N3
chr10:118363546-118363546p.W356C3
chr10:118354277-118354277p.C122C2
chr10:118355811-118355811p.T184I2
chr10:118354297-118354297p.S129F2
chr10:118364914-118364914p.G397S2
chr10:118360655-118360655p.R335S2
chr10:118354325-118354325p.N138K2
chr10:118354250-118354250p.F113F2
chr10:118351283-118351283p.G17E2

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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
# sample44 5  6 1  1451 1115 4
# mutation44 5  6 1  1571 1155 6
nonsynonymous SNV43 4  5    941  104 6
synonymous SNV 1 1  1 1  63  151  
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
chr10:118354250p.F113F3
chr10:118359629p.P295P2
chr10:118359630p.D296N2
chr10:118359613p.V147M1
chr10:118352022p.F230L1
chr10:118354358p.F343L1
chr10:118364906p.P466S1
chr10:118357378p.G53R1
chr10:118368610p.V147V1
chr10:118351338p.L231V1

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 PNLIPRP1 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 PNLIPRP1

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

BTBD17,CABS1,PPP1R17,CELA2B,CELA3A,CELA3B,CLPS,
CPA1,CPA2,CTRB1,CTRB2,CTRC,PLA2G1B,PNLIP,
PNLIPRP1,REG1B,REG1P,REG3A,SCGB3A1,SYCN,TBR1
ARGFX,LINC00293,BTLA,C9orf57,CACNG2,FCAMR,H1FOO,
LILRP2,LOC283663,NEUROG1,OR5B3,OR5C1,OR8G2,OR8I2,
OR8K1,PNLIPRP1,PRNT,SMEK3P,TCL6,ZIM3,ZNF679

AMY2A,C11orf40,CELA2A,CELA2B,CELA3A,CELA3B,CLPS,
CPA1,CTRB1,CTRB2,CTRC,CYP2A6,DUSP15,OPRM1,
PDYN,PLA2G1B,PNLIP,PNLIPRP1,PNLIPRP2,SYCN,ZNF280B
ARHGAP36,B3GALT5-AS1,SPTSSB,CLDN8,CRYBA2,CTSE,FBXO25,
FRZB,GGT7,GP2,HEPACAM2,IL1R2,KLK3,LOC284578,
NRAP,PNLIPRP1,RESP18,RETNLB,RIMS4,SCGB2A1,ZNF613
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 PNLIPRP1


There's no related Drug.
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Cross referenced IDs for PNLIPRP1
* 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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