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 GPCPD1

Basic gene info.	Gene symbol	GPCPD1
	Gene name	glycerophosphocholine phosphodiesterase GDE1 homolog (S. cerevisiae)
	Synonyms	GDE5\|GDPD6\|PREI4
	Cytomap	UCSC genome browser: 20p12.3
	Genomic location	chr20 :5525079-5591672
	Type of gene	protein-coding
	RefGenes	NM_019593.3,
	Ensembl id	ENSG00000125772
	Description	glycerophosphocholine phosphodiesterase GPCPD1glycerophosphodiester phosphodiesterase 5preimplantation protein 4putative glycerophosphocholine phosphodiesterase GPCPD1putative glycerophosphodiester phosphodiesterase 5
	Modification date	20141207
dbXrefs	MIM : 614124
	HGNC : HGNC
	Ensembl : ENSG00000125772
	HPRD : 10025
	Vega : OTTHUMG00000031806
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GPCPD1
	BioGPS: 56261
	Gene Expression Atlas: ENSG00000125772
	The Human Protein Atlas: ENSG00000125772
Pathway	NCI Pathway Interaction Database: GPCPD1
	KEGG: GPCPD1
	REACTOME: GPCPD1
	ConsensusPathDB
	Pathway Commons: GPCPD1
Metabolism	MetaCyc: GPCPD1
	HUMANCyc: GPCPD1
Regulation	Ensembl's Regulation: ENSG00000125772
	miRBase: chr20 :5,525,079-5,591,672
	TargetScan: NM_019593
	cisRED: ENSG00000125772
Context	iHOP: GPCPD1
	cancer metabolism search in PubMed: GPCPD1
	UCL Cancer Institute: GPCPD1
Assigned class in ccmGDB	C

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Phenotypic Information for GPCPD1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: GPCPD1
	Familial Cancer Database: GPCPD1

* 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_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: GPCPD1
	MedGen: GPCPD1 (Human Medical Genetics with Condition)
	ClinVar: GPCPD1
Phenotype	MGI: GPCPD1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GPCPD1

Mutations for GPCPD1

* 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

* 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	GPCPD1	chr20	5528206	5528226	GPCPD1	chr20	5540186	5540206

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 GPCPD1 related fusion information.

ID	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
BE763222	FSTL1	1	150	3	120113901	120114050	GPCPD1	138	189	20	5542846	5542897
AW813838	SYTL4	106	497	X	99971689	99972080	GPCPD1	489	674	20	5568688	5568875
AW889516	GPCPD1	13	224	20	5542846	5543057	FSTL1	212	394	3	120113901	120114083

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=41)	Stat. for Synonymous SNVs (# total SNVs=15)

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
chr20:5574004-5574004	p.R67H	3
chr20:5564963-5564963	p.E105K	2
chr20:5566845-5566845	p.P101L	2
chr20:5545686-5545686	p.Q436E	2
chr20:5559069-5559069	p.T221M	2
chr20:5556455-5556455	p.?	2
chr20:5564940-5564940	p.Q112Q	2
chr20:5539438-5539438	p.P520P	2
chr20:5559154-5559154	p.D193Y	2
chr20:5550821-5550821	p.D374V	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	1	1	1	7			1		2			8	1	1			5	6		8
# mutation	1	1	1	7			1		2			8	1	1			5	6		9
nonsynonymous SNV	1		1	5			1		2			7		1			5	4		7
synonymous SNV		1		2								1	1					2		2

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
chr20:5559069	p.T221M	2
chr20:5559154	p.D193Y	2
chr20:5574004	p.R67H	2
chr20:5560675	p.G527E	1
chr20:5542132	p.I458I	1
chr20:5556594	p.I219M	1
chr20:5560680	p.T411T	1
chr20:5547413	p.P396L	1
chr20:5556595	p.E187Q	1
chr20:5528342	p.H373Y	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 GPCPD1 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 GPCPD1

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


BCAP29,C20orf196,CASP10,CASP8,DNAJB3,ELL2,FRMD4B, FZD4,GPCPD1,ITGB6,KAT2B,LPAR6,LTF,MMP21, NUMB,PRKAA1,RALGAPA2,SLC28A3,SPTLC3,TC2N,UGT1A1	ATL2,CCDC14,CDK6,CHST9,DSC2,EML4,EPHA7, GPCPD1,ITPR2,LOC284578,LOC286467,MBTD1,PMS1,SLCO1A2, SNHG4,STX16,TAF4B,TET2,ZNF121,ZNF518A,ZNF562

C20orf196,C20orf96,CDS2,CRLS1,CSNK2A1,CSRP2BP,ESF1, FAM156A,FERMT1,GPCPD1,KANK1,MAVS,MCM8,PLCB4, SNRPB2,SPIN3,TASP1,TRMT6,ZCCHC3,ZNF133,ZNF343	ALOXE3,B4GALT6,VCPKMT,CACNB2,CDK17,E2F6,GJA1, GPCPD1,HNRNPDL,MAP3K14,NAA16,PHF20L1,PRR3,REV1, RPS6KB1,RUFY2,SENP2,U2SURP,UPF3A,ZMYM5,ZBTB18

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 GPCPD1

There's no related Drug.

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Cross referenced IDs for GPCPD1

* 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