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 GNPAT

Basic gene info.	Gene symbol	GNPAT
	Gene name	glyceronephosphate O-acyltransferase
	Synonyms	DAP-AT\|DAPAT\|DHAPAT
	Cytomap	UCSC genome browser: 1q42
	Genomic location	chr1 :231376918-231413719
	Type of gene	protein-coding
	RefGenes	NM_014236.3,
	Ensembl id	ENSG00000116906
	Description	DHAP-ATacyl-CoA:dihydroxyacetonephosphateacyltransferasedihydroxyacetone phosphate acyltransferaseglycerone-phosphate O-acyltransferase
	Modification date	20141207
dbXrefs	MIM : 602744
	HGNC : HGNC
	Ensembl : ENSG00000116906
	HPRD : 04120
	Vega : OTTHUMG00000038024
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GNPAT
	BioGPS: 8443
	Gene Expression Atlas: ENSG00000116906
	The Human Protein Atlas: ENSG00000116906
Pathway	NCI Pathway Interaction Database: GNPAT
	KEGG: GNPAT
	REACTOME: GNPAT
	ConsensusPathDB
	Pathway Commons: GNPAT
Metabolism	MetaCyc: GNPAT
	HUMANCyc: GNPAT
Regulation	Ensembl's Regulation: ENSG00000116906
	miRBase: chr1 :231,376,918-231,413,719
	TargetScan: NM_014236
	cisRED: ENSG00000116906
Context	iHOP: GNPAT
	cancer metabolism search in PubMed: GNPAT
	UCL Cancer Institute: GNPAT
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: GNPAT
	Familial Cancer Database: GNPAT

* 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
KEGG_GLYCEROPHOSPHOLIPID_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_PEROXISOMAL_LIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

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

Mutations for GNPAT

* 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

There's no intra-chromosomal structural variation.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	GNPAT	chr1	231396783	231396803		chr9	83731475	83731495

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 GNPAT 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
DA174856	PLP1	1	103	X	103031789	103031891	GNPAT	102	526	1	231410993	231413439
AW810786	GNPAT	6	210	1	231393186	231393390	GNPAT	203	534	1	231392635	231392966
AK023953	NFIA	586	870	1	61926695	61926976	GNPAT	871	2774	1	231398550	231413668

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=8

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=67)	Stat. for Synonymous SNVs (# total SNVs=14)

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

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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
chr1:231408064-231408064	p.V510A	5
chr1:231408063-231408063	p.V510I	3
chr1:231411021-231411021	p.Y600H	2
chr1:231408094-231408094	p.V520D	2
chr1:231377193-231377193	p.L23L	2
chr1:231411174-231411174	p.L623V	2
chr1:231403468-231403468	p.V366V	2
chr1:231398518-231398518	p.R163Q	2
chr1:231406610-231406610	p.S462S	2
chr1:231401902-231401902	p.E305E	2

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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=6

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		5	1	14	1		2		2			9	2	3		1	3	2	2	10
# mutation		5	1	9	1		2		2			9	2	3		1	3	2	2	15
nonsynonymous SNV		3	1	9	1		2		2			6	2	3		1	2	2	2	11
synonymous SNV		2										3					1			4

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
chr1:231408064	p.V510A	5
chr1:231406610	p.R270G	2
chr1:231401795	p.S462S	2
chr1:231403468	p.V366V	2
chr1:231401164	p.C73G	1
chr1:231410987	p.R248C	1
chr1:231403517	p.P430H	1
chr1:231396349	p.L611F	1
chr1:231401482	p.K90N	1
chr1:231410988	p.A431T	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 GNPAT 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 GNPAT

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


AHCTF1,AIDA,ARV1,SPRTN,C1orf131,COG2,EXOC8, FBXO28,FH,GGPS1,GNPAT,NUP133,RAB4A,RBM34, RFWD2,SRP9,TAF5L,TBCE,TFB2M,TOMM20,TSNAX	ACAT1,AK3,ATPAF1,TCAIM,CSDE1,DLD,GHITM, GKAP1,GNPAT,HADHB,HOXA10,HSPB6,ISCA1P1,NRD1, PGM1,PHYH,PPP3CB,RRAGD,SETD3,SUCLA2,TBX15

ARF1,SPRTN,C1orf131,C1orf27,C1orf43,COG2,GGPS1, GNPAT,MRPS14,NUP133,POLR3C,RAB3GAP2,RAB4A,RBM34, RCOR3,TATDN3,TBCE,TIPRL,TOMM20,TSNAX,UFC1	ARL3,CAMLG,CBY1,CRYZL1,EIF4A2,ELP2,FAM172A, FAM175A,MTFR1L,GNPAT,H2AFV,HIBADH,ISCU,LZTFL1, MEAF6,MFF,CMC4,POLR1D,RYK,TTC33,ZNF639

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 GNPAT

There's no related Drug.

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Cross referenced IDs for GNPAT

* 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