Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 symbol	PPM1L
	Gene name	protein phosphatase, Mg2+/Mn2+ dependent, 1L
	Synonyms	PP2C-epsilon\|PP2CE\|PPM1-LIKE
	Cytomap	UCSC genome browser: 3q26.1
	Genomic location	chr3 :160473995-160788817
	Type of gene	protein-coding
	RefGenes	NM_139245.2,
	Ensembl id	ENSG00000163590
	Description	PP2C epsilonProtein phosphatase 2C epsilon isoformprotein phosphatase 1Lprotein phosphatase 2C isoform epsilon
	Modification date	20141207
dbXrefs	MIM : 611931
	HGNC : HGNC
	HPRD : 17889
Protein	UniProt: Q5SGD2 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PPM1L
	BioGPS: 151742
	Gene Expression Atlas: ENSG00000163590
	The Human Protein Atlas: ENSG00000163590
Pathway	NCI Pathway Interaction Database: PPM1L
	KEGG: PPM1L
	REACTOME: PPM1L
	ConsensusPathDB
	Pathway Commons: PPM1L
Metabolism	MetaCyc: PPM1L
	HUMANCyc: PPM1L
Regulation	Ensembl's Regulation: ENSG00000163590
	miRBase: chr3 :160,473,995-160,788,817
	TargetScan: NM_139245
	cisRED: ENSG00000163590
Context	iHOP: PPM1L
	cancer metabolism search in PubMed: PPM1L
	UCL Cancer Institute: PPM1L
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for PPM1L(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_SPHINGOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM	611931; gene.
Orphanet
Disease	KEGG Disease: PPM1L
	MedGen: PPM1L (Human Medical Genetics with Condition)
	ClinVar: PPM1L
Phenotype	MGI: PPM1L (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	PPM1L	chr3	160651807	160651827	RSRC1	chr3	157833355	157833375
ovary	PPM1L	chr3	160726646	160726666	PPM1L	chr3	160730437	160730457

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PPM1L related fusion information.

Head Gene

Tail Gene

Accession

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

AK025676

RNF213

4031

78345693

78368151

PPM1L

4026

4050

160744481

160744505

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr3:160786805-160786805	p.R136*	6
chr3:160783285-160783285	p.N44N	3
chr3:160783254-160783254	p.S34L	2
chr3:160783226-160783226	p.D25Y	2
chr3:160783332-160783332	p.R60K	2
chr3:160786690-160786690	p.N97N	1
chr3:160783243-160783243	p.N30N	1
chr3:160786835-160786835	p.H146Y	1
chr3:160783336-160783336	p.K61K	1
chr3:160786714-160786714	p.I105I	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	2	4		9	1		1					10	3				9	2		7
# mutation	2	4		9	1		1					10	3				10	2		8
nonsynonymous SNV	1	3		7	1							7	2				4	1		7
synonymous SNV	1	1		2			1					3	1				6	1		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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr3:160783332	p.N209N	2
chr3:160783243	p.N223N	2
chr3:160783285	p.R239T	2
chr3:160783293	p.E79K	1
chr3:160474330	p.D204Y	1
chr3:160786714	p.F296L	1
chr3:160679655	p.E79E	1
chr3:160783305	p.D204E	1
chr3:160474331	p.S301A	1
chr3:160786750	p.K84N	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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