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 SC5D

Basic gene info.	Gene symbol	SC5D
	Gene name	sterol-C5-desaturase
	Synonyms	ERG3\|S5DES\|SC5DL
	Cytomap	UCSC genome browser: 11q23.3
	Genomic location	:-
	Type of gene	protein-coding
	RefGenes	NM_001024956.2, NM_006918.4,
	Ensembl id	N/A
	Description	3beta-hydroxysteroid-delta5-desaturaseC-5 sterol desaturasedelta(7)-sterol 5-desaturasefungal ERG3, delta-5-desaturase-likelathosterol 5-desaturaselathosterol dehydrogenaselathosterol oxidasesterol-C5-desaturase (ERG3 delta-5-desaturase homolog, S.
	Modification date	20141207
dbXrefs	MIM : 602286
	HGNC : HGNC
	HPRD : 09078
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SC5D
	BioGPS: 6309
	Gene Expression Atlas: N/A
	The Human Protein Atlas: N/A
Pathway	NCI Pathway Interaction Database: SC5D
	KEGG: SC5D
	REACTOME: SC5D
	ConsensusPathDB
	Pathway Commons: SC5D
Metabolism	MetaCyc: SC5D
	HUMANCyc: SC5D
Regulation	Ensembl's Regulation: N/A
	miRBase: :-
	TargetScan: NM_001024956
	cisRED: N/A
Context	iHOP: SC5D
	cancer metabolism search in PubMed: SC5D
	UCL Cancer Institute: SC5D
Assigned class in ccmGDB	C

Top

Phenotypic Information for SC5D(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SC5D
	Familial Cancer Database: SC5D

* 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
Nat Rev Drug Discovery, 2013, 12: 829, doi: 10.1038/nrd4145

Others
OMIM
Orphanet
Disease	KEGG Disease: SC5D
	MedGen: SC5D (Human Medical Genetics with Condition)
	ClinVar: SC5D
Phenotype	MGI: SC5D (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SC5D

Mutations for SC5D

* 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 SC5D 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

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

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=0

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=0)	Stat. for Synonymous SNVs (# total SNVs=0)
There's no ns-snv.	There's no s-snv.
Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	There's no inserted snv.

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

Top

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			10			2		1			6	1	1			2	4		3
# mutation	1			10			2		1			6	1	1			2	4		3
nonsynonymous SNV	1			9					1			6	1				2	3		3
synonymous SNV				1			2							1				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])

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
chr11:121174120	p.V120A,SC5D	2
chr11:121177110	p.F12L,SC5D	2
chr11:121174140	p.R214H,SC5D	1
chr11:121177782	p.D26H,SC5D	1
chr11:121178097	p.F222C,SC5D	1
chr11:121174160	p.V40A,SC5D	1
chr11:121177854	p.F235L,SC5D	1
chr11:121178115	p.S53I,SC5D	1
chr11:121174203	p.F236F,SC5D	1
chr11:121177872	p.V57V,SC5D	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 SC5D 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 SC5D

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


ACSM1,ACSM3,ADH1C,AKR1B15,AKR1D1,EYS,IDI1, ISX,KPNA7,LOC255167,LOC91948,LST-3TM12,MYOM2,RLN3, RNASE11,RNASE12,SC5D,SCP2,SPINK8,SULT1C3,WDR64	ABCC11,ACSL3,ADAM2,ALOX15B,C15orf43,CCDC15,EPS8L3, FADS2,HPGD,IDI1,IYD,LONP2,LST-3TM12,MPV17L, PNLIPRP3,SC5D,SCP2,SERHL,SULT1C3,TMPRSS11F,UGT2B11

AASDHPPT,ACAT2,CYP51A1,DHCR7,HMGCR,HMGCS1,HSD17B12, IDH1,IDI1,LOC653566,MOB4,MRPL49,PPP2R1B,RAB6A, MSMO1,SC5D,SPCS2,SQLE,TMEM126B,TMEM135,TMEM41B	C14orf1,FDPS,GRB14,HMGCS1,HSD17B7,IDI1,INSIG1, MKX,NSDHL,PAQR9,PART1,PLA2G3,PRND,RDH11, RHAG,MSMO1,SC5D,SQLE,STARD4,TMEM232,TMPRSS11F

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 SC5D

There's no related Drug.

Top

Cross referenced IDs for SC5D

* 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