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

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 PGAP1

Basic gene info.	Gene symbol	PGAP1
	Gene name	post-GPI attachment to proteins 1
	Synonyms	Bst1\|ISPD3024\|MRT42\|SPG67
	Cytomap	UCSC genome browser: 2q33.1
	Genomic location	chr2 :197697727-197791454
	Type of gene	protein-coding
	RefGenes	NM_024989.3,
	Ensembl id	ENSG00000197121
	Description	GPI deacylaseGPI inositol-deacylasehPGAP1post-GPI attachment to proteins factor 1
	Modification date	20141207
dbXrefs	MIM : 611655
	HGNC : HGNC
	Ensembl : ENSG00000197121
	HPRD : 10147
	Vega : OTTHUMG00000132743
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PGAP1
	BioGPS: 80055
	Gene Expression Atlas: ENSG00000197121
	The Human Protein Atlas: ENSG00000197121
Pathway	NCI Pathway Interaction Database: PGAP1
	KEGG: PGAP1
	REACTOME: PGAP1
	ConsensusPathDB
	Pathway Commons: PGAP1
Metabolism	MetaCyc: PGAP1
	HUMANCyc: PGAP1
Regulation	Ensembl's Regulation: ENSG00000197121
	miRBase: chr2 :197,697,727-197,791,454
	TargetScan: NM_024989
	cisRED: ENSG00000197121
Context	iHOP: PGAP1
	cancer metabolism search in PubMed: PGAP1
	UCL Cancer Institute: PGAP1
Assigned class in ccmGDB	C

Top

Phenotypic Information for PGAP1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PGAP1
	Familial Cancer Database: PGAP1

* 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_METABOLISM_OF_PROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: PGAP1
	MedGen: PGAP1 (Human Medical Genetics with Condition)
	ClinVar: PGAP1
Phenotype	MGI: PGAP1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PGAP1

Mutations for PGAP1

* 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

Top

- 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
ovary	PGAP1	chr2	197715063	197715083	PGAP1	chr2	197723435	197723455
ovary	PGAP1	chr2	197740467	197740487	PGAP1	chr2	197740785	197740805
ovary	PGAP1	chr2	197791414	197791434	STK35	chr20	2108678	2108698

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 PGAP1 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

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

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)

Top

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

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=82)	Stat. for Synonymous SNVs (# total SNVs=10)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=2)

Top

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
chr2:197712711-197712711	p.K638E	3
chr2:197737199-197737199	p.F565C	3
chr2:197761878-197761878	p.L302F	2
chr2:197740525-197740525	p.F457L	2
chr2:197761892-197761892	p.R297Q	2
chr2:197744810-197744810	p.R447H	2
chr2:197712713-197712713	p.Y637C	2
chr2:197767305-197767305	p.?	2
chr2:197757952-197757952	p.K315N	2
chr2:197755595-197755595	p.H377R	2

Top

SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1	6		12			4		2	2		7	4	7			7	9		17
# mutation	1	6		12			4		2	2		7	5	6			7	9		21
nonsynonymous SNV	1	5		10			1		2	2		6	5	5			5	8		18
synonymous SNV		1		2			3					1		1			2	1		3

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])

Top

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
chr2:197737199	p.F565C	3
chr2:197757952	p.K315N	2
chr2:197761892	p.R297Q	2
chr2:197712711	p.K638E	2
chr2:197711732	p.E44K	1
chr2:197767380	p.R785G	1
chr2:197781209	p.P599S	1
chr2:197708759	p.V320V	1
chr2:197757891	p.P165S	1
chr2:197784857	p.W26C	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 PGAP1 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]

Top

Gene Expression for PGAP1

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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

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


ABI2,ALS2,ERCC6L2,CREB1,DCAF17,FOXP2,GTF3C3, KLHL23,LANCL1,MIB1,PGAP1,PIKFYVE,PLEKHM3,RIF1, SLC30A4,SP4,STAG2,TTBK2,TTC21B,VPS13A,ZKSCAN8	CARF,ARHGAP5,BBX,C11orf30,PCNXL4,CCNT2,CCP110, DCAF17,GOPC,GLTSCR1L,MIB1,KMT2E,NFAT5,PDS5B, PGAP1,PHIP,RALGAPA1,RBM26,RICTOR,ZMYM1,ZNF292

B3GALNT2,BCL9,C2orf66,KANSL1L,CHRM3,KDM5B,KIAA1804, NUCKS1,PGAP1,PIK3C2B,PLEKHA6,POGZ,RAB4A,RCOR3, RPRD2,SATB1,TPR,WDR26,ZC3H11A,ZNF33A,ZNF792	ADAMTS5,ARID1B,ARID5B,ATP7A,BAHCC1,CACHD1,HOXA2, LINC00312,MEX3A,NOTCH3,NOV,NTRK3,PGAP1,POM121, RASAL2,RGPD6,RHOBTB3,SYT2,TUG1,UTRN,ZNF121

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

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for PGAP1

There's no related Drug.

Top

Cross referenced IDs for PGAP1

* 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