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 PEMT
Basic gene info.Gene symbolPEMT
Gene namephosphatidylethanolamine N-methyltransferase
SynonymsPEAMT|PEMPT|PEMT2|PNMT
CytomapUCSC genome browser: 17p11.2
Genomic locationchr17 :17408876-17485745
Type of geneprotein-coding
RefGenesNM_001267551.1,
NM_001267552.1,NM_007169.2,NM_148172.2,NM_148173.1,
Ensembl idENSG00000133027
Description-
Modification date20141207
dbXrefs MIM : 602391
HGNC : HGNC
Ensembl : ENSG00000133027
HPRD : 03862
Vega : OTTHUMG00000059290
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PEMT
BioGPS: 10400
Gene Expression Atlas: ENSG00000133027
The Human Protein Atlas: ENSG00000133027
PathwayNCI Pathway Interaction Database: PEMT
KEGG: PEMT
REACTOME: PEMT
ConsensusPathDB
Pathway Commons: PEMT
MetabolismMetaCyc: PEMT
HUMANCyc: PEMT
RegulationEnsembl's Regulation: ENSG00000133027
miRBase: chr17 :17,408,876-17,485,745
TargetScan: NM_001267551
cisRED: ENSG00000133027
ContextiHOP: PEMT
cancer metabolism search in PubMed: PEMT
UCL Cancer Institute: PEMT
Assigned class in ccmGDBC

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

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

Mutations for PEMT
* 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
central_nervous_systemPEMTchr171742275717422757PEMTchr171743235417432354
ovaryPEMTchr171746455617464576chr177963373379633753
pancreasPEMTchr171745641317456433chr206291404362914063
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 PEMT related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA035445PEMT134154171742704617427066SCNN1A1383681264571856457412

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 # sample1                
GAIN (# sample)                 
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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=11)
Stat. for Synonymous SNVs
(# total SNVs=5)
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
chr17:17415867-17415867p.V141A2
chr17:17409560-17409560p.V212M2
chr17:17425608-17425608p.F102F2
chr17:17480323-17480323p.T39S1
chr17:17409144-17409144p.I224M1
chr17:17415878-17415878p.G137G1
chr17:17494875-17494875p.C22C1
chr17:17409545-17409545p.E217K1
chr17:17425604-17425604p.R104C1
chr17:17494926-17494926p.G5G1

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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
# sample   3  1 1  1   241 1
# mutation   3  1 1  1   231 1
nonsynonymous SNV   2       1   121 1
synonymous SNV   1  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
chr17:17425608p.F80F,PEMT2
chr17:17425685p.S208S,PEMT1
chr17:17409126p.E195K,PEMT1
chr17:17425706p.V190M,PEMT1
chr17:17409545p.N155S,PEMT1
chr17:17480299p.P149S,PEMT1
chr17:17409560p.T146I,PEMT1
chr17:17412796p.A143A,PEMT1
chr17:17412815p.F137F,PEMT1
chr17:17412823p.P64P,PEMT1

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 PEMT 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 PEMT

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

ARL2,C17orf49,C1orf86,C9orf16,CCDC85B,DRG2,CTDNEP1,
ABHD17A,NAA38,MAP2K2,MBD3,MED9,NDUFA11,NT5M,
PEMT,PLIN4,PSMB6,RDH5,RNASEK,TRAPPC1,ZSWIM7
ANKDD1A,ARHGDIG,CCDC107,DMTN,FADS3,FSTL3,ITGB5,
ITIH5,ITPK1,MMP28,MSC,PEMT,PEPD,PMEPA1,
RAB3C,RHOXF1,SLC35C1,SRPX2,TMEM189,TPST2,ZNF541

ATPAF2,C17orf49,ELP5,C1QBP,COPS3,DRG2,NAA38,
MED11,MED9,LRRC75A-AS1,PEMT,PRPSAP2,PSMB6,RANGRF,
RNF167,RPAIN,SLC25A11,STX8,TRAPPC1,UBB,YWHAE
AHCY,APEX1,MRPS26,PEMT,RPL10,RPL10A,RPL18A,
RPL19,RPL29,RPL3,RPL7A,RPL8,RPLP0,RPS3,
RPS5,RPSAP58,RPUSD4,SUMF2,TMEM5,TTC5,ZNF511
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 PEMT


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