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 DHPS

Basic gene info.	Gene symbol	DHPS
	Gene name	deoxyhypusine synthase
	Synonyms	DHS\|DS\|MIG13
	Cytomap	UCSC genome browser: 19p13.2
	Genomic location	chr19 :12786530-12792025
	Type of gene	protein-coding
	RefGenes	NM_001206974.1, NM_001930.3,NM_013406.2,NR_038192.1,NM_013407.1,
	Ensembl id	ENSG00000095059
	Description	migration-inducing gene 13
	Modification date	20141207
dbXrefs	MIM : 600944
	HGNC : HGNC
	Ensembl : ENSG00000095059
	HPRD : 02969
	Vega : OTTHUMG00000182618
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_DHPS
	BioGPS: 1725
	Gene Expression Atlas: ENSG00000095059
	The Human Protein Atlas: ENSG00000095059
Pathway	NCI Pathway Interaction Database: DHPS
	KEGG: DHPS
	REACTOME: DHPS
	ConsensusPathDB
	Pathway Commons: DHPS
Metabolism	MetaCyc: DHPS
	HUMANCyc: DHPS
Regulation	Ensembl's Regulation: ENSG00000095059
	miRBase: chr19 :12,786,530-12,792,025
	TargetScan: NM_001206974
	cisRED: ENSG00000095059
Context	iHOP: DHPS
	cancer metabolism search in PubMed: DHPS
	UCL Cancer Institute: DHPS
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: DHPS
	Familial Cancer Database: DHPS

* 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: DHPS
	MedGen: DHPS (Human Medical Genetics with Condition)
	ClinVar: DHPS
Phenotype	MGI: DHPS (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: DHPS

Mutations for DHPS

* 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 DHPS 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
CV364179	DHPS	1	357	19	12790436	12791114	DHPS	351	456	19	12792579	12792684
BQ436553	WDR83	1	231	19	12786543	12786856	DHPS	228	350	19	12790971	12791093

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

There's no copy number variation information in COSMIC data for this gene.

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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=23)	Stat. for Synonymous SNVs (# total SNVs=14)

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
chr19:12792434-12792434	p.F49F	4
chr19:12792377-12792377	p.A68A	2
chr19:12786945-12786945	p.A300A	2
chr19:12788187-12788187	p.P234P	2
chr19:12790661-12790661	p.E150K	2
chr19:12790678-12790678	p.A144V	1
chr19:12786738-12786738	p.D342N	1
chr19:12791116-12791116	p.L77L	1
chr19:12790301-12790301	p.N216K	1
chr19:12790704-12790704	p.V135V	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	3		6								4					3	4		6
# mutation	1	3		5								4					3	4		8
nonsynonymous SNV	1	2		2								2					1	2		7
synonymous SNV		1		3								2					2	2		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
chr19:12790515	p.V129V,DHPS	2
chr19:12792409	p.A258A,DHPS	1
chr19:12786878	p.I66M,DHPS	1
chr19:12790530	p.C233Y,DHPS	1
chr19:12792434	p.R49H,DHPS	1
chr19:12786945	p.G200G,DHPS	1
chr19:12790661	p.D44N,DHPS	1
chr19:12792443	p.L199L,DHPS	1
chr19:12787986	p.L35L,DHPS	1
chr19:12790732	p.D196D,DHPS	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 DHPS 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 DHPS

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


AP1M2,ASNA1,ATG4D,C12orf10,WDR83OS,DHPS,ECSIT, EIF3G,ELOF1,FARSA,FBXW9,GCDH,NDUFA7,PIN1, PRDX2,QTRT1,RAD23A,TMED1,WDR83,ZNF414,ZNF653	ACTR1B,ALKBH7,ATPAF2,RPP25L,CECR5,CPSF3L,DHPS, ECSIT,EIF3G,GCAT,NPRL2,NSUN5,PMPCA,POLR2I, PTOV1,RNMTL1,SDR39U1,SGTA,MIEF2,THAP4,TIMM17B

ALKBH7,ATG4D,WDR83OS,C19orf70,COPE,DHPS,ECSIT, EIF3G,FAU,GADD45GIP1,NDUFA13,NDUFA7,NDUFB7,PIN1, RPS15,TECR,TMED1,TRAPPC5,TRPT1,UBA52,UQCR11	ATP5G2,BTF3,C12orf10,C12orf57,C15orf61,WDR83OS,DGCR6L, DHPS,DRG2,ERCC1,ING4,KLHDC3,MPG,MRPL43, RPL18,RPL29,RPL8,SDHAF1,SUMF2,TMEM42,WBP1

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 DHPS

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
DB01907	deoxyhypusine synthase	experimental	Nicotinamide-Adenine-Dinucleotide
DB03639	deoxyhypusine synthase	experimental	1-Guanidinium-7-Aminoheptane
DB01033	deoxyhypusine synthase	approved	Mercaptopurine
DB00563	deoxyhypusine synthase	approved	Methotrexate

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Cross referenced IDs for DHPS

* 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