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 PPM1L
Basic gene info.Gene symbolPPM1L
Gene nameprotein phosphatase, Mg2+/Mn2+ dependent, 1L
SynonymsPP2C-epsilon|PP2CE|PPM1-LIKE
CytomapUCSC genome browser: 3q26.1
Genomic locationchr3 :160473995-160788817
Type of geneprotein-coding
RefGenesNM_139245.2,
Ensembl idENSG00000163590
DescriptionPP2C epsilonProtein phosphatase 2C epsilon isoformprotein phosphatase 1Lprotein phosphatase 2C isoform epsilon
Modification date20141207
dbXrefs MIM : 611931
HGNC : HGNC
HPRD : 17889
ProteinUniProt: Q5SGD2
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PPM1L
BioGPS: 151742
Gene Expression Atlas: ENSG00000163590
The Human Protein Atlas: ENSG00000163590
PathwayNCI Pathway Interaction Database: PPM1L
KEGG: PPM1L
REACTOME: PPM1L
ConsensusPathDB
Pathway Commons: PPM1L
MetabolismMetaCyc: PPM1L
HUMANCyc: PPM1L
RegulationEnsembl's Regulation: ENSG00000163590
miRBase: chr3 :160,473,995-160,788,817
TargetScan: NM_139245
cisRED: ENSG00000163590
ContextiHOP: PPM1L
cancer metabolism search in PubMed: PPM1L
UCL Cancer Institute: PPM1L
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PPM1L(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PPM1L
Familial Cancer Database: PPM1L
* 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_PHOSPHOLIPID_METABOLISM
REACTOME_SPHINGOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 611931; gene.
Orphanet
DiseaseKEGG Disease: PPM1L
MedGen: PPM1L (Human Medical Genetics with Condition)
ClinVar: PPM1L
PhenotypeMGI: PPM1L (International Mouse Phenotyping Consortium)
PhenomicDB: PPM1L

Mutations for PPM1L
* 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
ovaryPPM1Lchr3160651807160651827RSRC1chr3157833355157833375
ovaryPPM1Lchr3160726646160726666PPM1Lchr3160730437160730457
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 PPM1L related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AK025676RNF21314031177834569378368151PPM1L402640503160744481160744505

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 # sample3 11    4 2      
GAIN (# sample)2 11    4 2      
LOSS (# sample)1                
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=32)
Stat. for Synonymous SNVs
(# total SNVs=6)
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
chr3:160786805-160786805p.R136*6
chr3:160783285-160783285p.N44N3
chr3:160783226-160783226p.D25Y2
chr3:160783332-160783332p.R60K2
chr3:160783254-160783254p.S34L2
chr3:160786750-160786750p.F117L1
chr3:160783260-160783260p.G36V1
chr3:160786870-160786870p.F157F1
chr3:160786635-160786635p.Q79L1
chr3:160786763-160786763p.S122A1

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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
# sample24 91 1    103   92 7
# mutation24 91 1    103   102 8
nonsynonymous SNV13 71      72   41 7
synonymous SNV11 2  1    31   61 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
chr3:160783332p.R239T2
chr3:160783243p.N209N2
chr3:160783285p.N223N2
chr3:160474333p.R108P1
chr3:160786763p.P226L1
chr3:160679684p.G327V1
chr3:160783336p.L115P1
chr3:160474348p.D230A1
chr3:160786769p.F336F1
chr3:160783197p.I126M1

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 PPM1L 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 PPM1L

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

ASXL2,CNOT1,EML4,GAN,IPMK,KIAA0754,KIF1B,
LOC284441,NMD3,NPAT,PAFAH1B2,PPM1L,RIF1,ROCK2,
SHPRH,SLC30A6,STRN,UBXN7,USP34,ZDHHC20,ZFR
DIAPH2,EXOC6B,FOXN3,HIPK3,IGF2R,KIAA1715,LIMS1,
LNPEP,MAN2A2,MPP6,NEK9,PARD3B,PCYT1A,PPM1L,
RNF150,SAMD8,SETD7,TEAD1,TRIP12,USP9X,YPEL2

AKAP13,CCDC186,C11orf30,CEP97,DAAM1,EP300,FAM168A,
FAM63B,GTF2A1,KIAA1244,LRCH3,MAGI1,MAN1A2,N4BP2,
NHLRC2,PPM1L,RNF168,STXBP5,TET2,TRIP11,ZFP91
AHNAK,SOGA1,COL8A1,DLG5,ERC1,EVC,FN1,
FYCO1,HDAC4,ITGA9,MACF1,NAV2,NFIC,NHSL2,
PARD3B,PPM1L,PTPN14,ROR1,SACS,SYNE1,ZC3H13
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 PPM1L


There's no related Drug.
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Cross referenced IDs for PPM1L
* 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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