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 PTDSS1

Basic gene info.	Gene symbol	PTDSS1
	Gene name	phosphatidylserine synthase 1
	Synonyms	LMHD\|PSS1\|PSSA
	Cytomap	UCSC genome browser: 8q22
	Genomic location	chr8 :97274166-97346774
	Type of gene	protein-coding
	RefGenes	NM_001290225.1, NM_014754.2,
	Ensembl id	ENSG00000156471
	Description	PSS-1ptdSer synthase 1serine-exchange enzyme I
	Modification date	20141207
dbXrefs	MIM : 612792
	HGNC : HGNC
	HPRD : 17926
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PTDSS1
	BioGPS: 9791
	Gene Expression Atlas: ENSG00000156471
	The Human Protein Atlas: ENSG00000156471
Pathway	NCI Pathway Interaction Database: PTDSS1
	KEGG: PTDSS1
	REACTOME: PTDSS1
	ConsensusPathDB
	Pathway Commons: PTDSS1
Metabolism	MetaCyc: PTDSS1
	HUMANCyc: PTDSS1
Regulation	Ensembl's Regulation: ENSG00000156471
	miRBase: chr8 :97,274,166-97,346,774
	TargetScan: NM_001290225
	cisRED: ENSG00000156471
Context	iHOP: PTDSS1
	cancer metabolism search in PubMed: PTDSS1
	UCL Cancer Institute: PTDSS1
Assigned class in ccmGDB	C

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Phenotypic Information for PTDSS1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PTDSS1
	Familial Cancer Database: PTDSS1

* 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_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: PTDSS1
	MedGen: PTDSS1 (Human Medical Genetics with Condition)
	ClinVar: PTDSS1
Phenotype	MGI: PTDSS1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PTDSS1

Mutations for PTDSS1

* 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

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 PTDSS1 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
BE677852	PTDSS1	5	132	8	97346653	97346780	PTDSS1	130	357	8	97346007	97346234
AL589407	WSCD1	1	313	17	6002153	6002468	PTDSS1	309	492	8	97315086	97315269

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=60)	Stat. for Synonymous SNVs (# total SNVs=17)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	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
chr8:97345750-97345750	p.R460W	3
chr8:97332566-97332566	p.L389R	2
chr8:97321823-97321823	p.R349H	2
chr8:97342499-97342499	p.H411R	2
chr8:97321836-97321836	p.Q353Q	2
chr8:97285569-97285569	p.L74L	2
chr8:97318750-97318750	p.L325I	2
chr8:97311998-97311998	p.N226S	2
chr8:97316364-97316364	p.S283S	1
chr8:97345714-97345714	p.G448C	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	3		13	3		4		2			14	5	1	1	1	2	4		6
# mutation	2	3		12	3		4		2			15	6	1	1	1	2	4		7
nonsynonymous SNV	2	2		10	3		4		2			11	4	1	1	1		2		5
synonymous SNV		1		2								4	2				2	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
chr8:97316287	p.N80S,PTDSS1	2
chr8:97342499	p.R314W,PTDSS1	2
chr8:97311998	p.G112W,PTDSS1	2
chr8:97299302	p.F123F	2
chr8:97345750	p.H265R,PTDSS1	2
chr8:97332520	p.C79Y,PTDSS1	1
chr8:97307339	p.V189V,PTDSS1	1
chr8:97345788	p.K268N,PTDSS1	1
chr8:97318782	p.S52S	1
chr8:97274424	p.Y193Y,PTDSS1	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 PTDSS1 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 PTDSS1

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


CHMP4C,DCAF13,DSCC1,EIF3E,ESRP1,INTS8,MRPL15, MTDH,MTERF3,MTFR1,NUDCD1,PABPC1,POP1,PTDSS1, RAD54B,SLC25A32,TGS1,EMC2,UBE2V2,YWHAZ,ZFAND1	APEX1,GID8,CHMP4C,CSTF1,DKC1,GINS2,ILF2, NONO,NPM1,PABPC1,PGAP2,PRMT5,PTDSS1,RAE1, RFC5,RPLP0,RPS4X,SET,SSR2,NELFCD,XRCC5

HGH1,C8orf33,NDUFAF6,CHRAC1,CSPP1,DCAF13,DSCC1, FAM91A1,INTS8,KIAA1429,MTDH,MTERF3,MTFR1,NUDCD1, OTUD6B,PTDSS1,PUF60,RRS1,SLC25A32,EMC2,UTP23	CCT8,FARSB,FBL,GEMIN4,IMPDH2,LARS,MRPL37, MRPS2,MRPS30,MRPS9,NARS2,NOP14,PPIF,PTDSS1, RNMTL1,SHMT2,TMEM5,TRAP1,TSFM,UMPS,UNG

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 PTDSS1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00144	phosphatidylserine synthase 1	approved; nutraceutical	Phosphatidylserine

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Cross referenced IDs for PTDSS1

* 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