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 DEGS1

Basic gene info.	Gene symbol	DEGS1
	Gene name	delta(4)-desaturase, sphingolipid 1
	Synonyms	DEGS\|DEGS-1\|DES1\|Des-1\|FADS7\|MLD
	Cytomap	UCSC genome browser: 1q42.11
	Genomic location	chr1 :224370909-224381142
	Type of gene	protein-coding
	RefGenes	NM_144780.1, NM_003676.3,
	Ensembl id	ENSG00000143753
	Description	cell migration-inducing gene 15 proteindegenerative spermatocyte homolog 1, lipid desaturasedegenerative spermatocyte homolog, lipid desaturasedihydroceramide desaturase 1membrane fatty acid (lipid) desaturasemembrane lipid desaturasemigration-induc
	Modification date	20141207
dbXrefs	MIM : 615843
	HGNC : HGNC
	Ensembl : ENSG00000143753
	HPRD : 13133
	Vega : OTTHUMG00000037496
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_DEGS1
	BioGPS: 8560
	Gene Expression Atlas: ENSG00000143753
	The Human Protein Atlas: ENSG00000143753
Pathway	NCI Pathway Interaction Database: DEGS1
	KEGG: DEGS1
	REACTOME: DEGS1
	ConsensusPathDB
	Pathway Commons: DEGS1
Metabolism	MetaCyc: DEGS1
	HUMANCyc: DEGS1
Regulation	Ensembl's Regulation: ENSG00000143753
	miRBase: chr1 :224,370,909-224,381,142
	TargetScan: NM_144780
	cisRED: ENSG00000143753
Context	iHOP: DEGS1
	cancer metabolism search in PubMed: DEGS1
	UCL Cancer Institute: DEGS1
Assigned class in ccmGDB	C

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Phenotypic Information for DEGS1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: DEGS1
	Familial Cancer Database: DEGS1

* 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_SPHINGOLIPID_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_SPHINGOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: DEGS1
	MedGen: DEGS1 (Human Medical Genetics with Condition)
	ClinVar: DEGS1
Phenotype	MGI: DEGS1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: DEGS1

Mutations for DEGS1

* 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

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

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows DEGS1 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
BF944194	DEGS1	24	243	1	224377512	224377733	DMPK	243	402	19	46283369	46283522
BG249152	DEGS1	1	60	1	224377865	224377924	SERINC1	58	753	6	122765667	122767951
AI167570	DEGS1	1	181	1	224379907	224380087	CDC73	178	478	1	193189506	193189807
AL079576	DEGS1	41	108	1	224377681	224377748	DEGS1	104	331	1	224377728	224377955

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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=29)	Stat. for Synonymous SNVs (# total SNVs=2)

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
chr1:224371065-224371065	p.D9E	2
chr1:224377819-224377819	p.S208Y	2
chr1:224377462-224377462	p.H89R	1
chr1:224377686-224377686	p.I164V	1
chr1:224377867-224377867	p.P224L	1
chr1:224377484-224377484	p.A96A	1
chr1:224377699-224377699	p.L168H	1
chr1:224377904-224377904	p.F236L	1
chr1:224377500-224377500	p.A102T	1
chr1:224377714-224377714	p.R173Q	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=1

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		3		2			1		3			3	1				1	2		4
# mutation		3		2			1		3			3	1				1	2		6
nonsynonymous SNV		3		2			1		3			3	1				1	2		4
synonymous SNV																				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
chr1:224377500	p.D63Y	1
chr1:224377848	p.K313N	1
chr1:224377616	p.A102T	1
chr1:224377867	p.V140V	1
chr1:224377623	p.D143N	1
chr1:224378005	p.E149D	1
chr1:224371065	p.K159R	1
chr1:224377643	p.I164V	1
chr1:224380110	p.R173Q	1
chr1:224377282	p.T183T	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 DEGS1 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 DEGS1

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


ABCC6P2,CALCR,CNIH4,DEGS1,ENAH,EPHX1,FBXO28, GGPS1,GHITM,GRIP1,MSLNL,NVL,NXPH2,OMG, OR2AT4,PAX7,SLC12A8,SRP9,ST6GAL1,TMEM159,WDR26	ANXA1,ARF4,ARL2BP,ATP6AP2,DTD2,TPGS2,C1orf198, CALM2,CCNY,CMPK1,DEGS1,ETF1,MAPRE1,PPA1, PPP2CB,PWP1,RAB1A,RAB9A,RAP1B,SLC25A43,UBE2E2

AIDA,MSANTD3,CALU,CHST15,COPZ2,DEGS1,DYRK3, EHD2,EMP3,GPX8,IKBIP,JAZF1,KLHL5,LGALS1, MSN,PEA15,PRKCDBP,PTRF,SELM,SRGAP2,TIMP1	ARL4D,CLMP,BAG2,CALU,CCDC69,CFL2,DEGS1, DTNA,GUCY1B3,KCNJ8,PEA15,PLEKHO1,RAB31,RAB34, RAMP1,RASSF8,RPS6KC1,SCRG1,SELM,TEAD2,TMEM55A

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 DEGS1

There's no related Drug.

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Cross referenced IDs for DEGS1

* 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