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 DHCR24

Basic gene info.	Gene symbol	DHCR24
	Gene name	24-dehydrocholesterol reductase
	Synonyms	DCE\|Nbla03646\|SELADIN1\|seladin-1
	Cytomap	UCSC genome browser: 1p32.3
	Genomic location	chr1 :55315299-55352921
	Type of gene	protein-coding
	RefGenes	NM_014762.3,
	Ensembl id	ENSG00000116133
	Description	3 beta-hydroxysterol delta 24-reductase3-beta-hydroxysterol delta-24-reductasedelta(24)-sterol reductasedesmosterol-to-cholesterol enzymediminuto/dwarf1 homologseladin 1selective AD indicator 1
	Modification date	20141207
dbXrefs	MIM : 606418
	HGNC : HGNC
	Ensembl : ENSG00000116133
	HPRD : 05916
	Vega : OTTHUMG00000009989
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_DHCR24
	BioGPS: 1718
	Gene Expression Atlas: ENSG00000116133
	The Human Protein Atlas: ENSG00000116133
Pathway	NCI Pathway Interaction Database: DHCR24
	KEGG: DHCR24
	REACTOME: DHCR24
	ConsensusPathDB
	Pathway Commons: DHCR24
Metabolism	MetaCyc: DHCR24
	HUMANCyc: DHCR24
Regulation	Ensembl's Regulation: ENSG00000116133
	miRBase: chr1 :55,315,299-55,352,921
	TargetScan: NM_014762
	cisRED: ENSG00000116133
Context	iHOP: DHCR24
	cancer metabolism search in PubMed: DHCR24
	UCL Cancer Institute: DHCR24
Assigned class in ccmGDB	C

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Phenotypic Information for DHCR24(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: DHCR24
	Familial Cancer Database: DHCR24

* 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_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: DHCR24
	MedGen: DHCR24 (Human Medical Genetics with Condition)
	ClinVar: DHCR24
Phenotype	MGI: DHCR24 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: DHCR24

Mutations for DHCR24

* 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

There's no inter-chromosomal structural variation.

- For Intra-chromosomal Variations

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
prostate	DHCR24	chr1	55331647	55331647	OPTC	chr1	203467515	203467515

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 DHCR24 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
BE828048	CNPPD1	3	274	2	220036940	220037211	DHCR24	265	380	1	55315314	55315429
DB244252	GAS5	1	78	1	173833503	173833579	DHCR24	74	560	1	55316353	55316839
DA340395	LOC100507412	1	174	?	115720	115893	DHCR24	174	569	1	55349393	55352903
DA046822	FAM105A	1	188	5	14610382	14610569	DHCR24	189	738	1	55317014	55317563
AA658920	DHCR24	8	146	1	55316129	55316267	DHCR24	144	527	1	55316263	55316646
AW997410	DHCR24	1	135	1	55319150	55319284	QSOX2	127	147	9	139118628	139118648
BF918420	ZNF276	14	86	16	89806615	89806687	DHCR24	82	394	1	55316392	55316704
AI207637	DHCR24	1	533	1	55316503	55317035	B4GALT5	518	631	20	48252183	48252296
AW997408	DHCR24	5	126	1	55319162	55319284	QSOX2	118	138	9	139118628	139118648
AI369276	USP22	1	283	17	20903048	20903330	DHCR24	279	375	1	55352289	55352385

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=21)	Stat. for Synonymous SNVs (# total SNVs=12)

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
chr1:55319719-55319719	p.N403N	3
chr1:55352725-55352725	p.L23Q	2
chr1:55337260-55337260	p.A213A	2
chr1:55337094-55337094	p.G269R	2
chr1:55341714-55341714	p.R132C	2
chr1:55319845-55319845	p.P361P	1
chr1:55349447-55349447	p.?	1
chr1:55337114-55337114	p.Q262R	1
chr1:55317977-55317977	p.R494*	1
chr1:55349311-55349311	p.E123K	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	2	4	1	2								2		1			2	5		5
# mutation	3	4	1	2								2		1			2	5		8
nonsynonymous SNV	2	3	1	2								2		1			1	3		5
synonymous SNV	1	1															1	2		3

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
chr1:55319868	p.R478Q	1
chr1:55337260	p.L293L	1
chr1:55318024	p.V464M	1
chr1:55331007	p.Q262R	1
chr1:55340771	p.D436N	1
chr1:55319114	p.H257H	1
chr1:55331027	p.P414Q	1
chr1:55340859	p.Y237Y	1
chr1:55319198	p.H406Q	1
chr1:55331049	p.A226A	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 DHCR24 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 DHCR24

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


ABCD3,ACACA,AHCYL1,CA12,CMBL,CPT2,DHCR24, ELOVL5,FLNB,HMGCR,HSD3B2,MCCC2,RAB5B,REEP5, RETSAT,MSMO1,SCD,SCP2,TMBIM6,TMEM59,YIPF1	ACPP,ALDH3B2,ATP2C2,CYP4Z2P,DHCR24,FAM174B,GPR39, HMGCS2,HRASLS2,CERS4,LPCAT3,MOGAT2,PON3,PTPLAD1, PXMP4,REEP6,SLC38A1,SLC7A8,SULT2B1,TMEM45B,TMEM63C

ACAT2,ACOT11,CDCA8,CYP51A1,DHCR24,DHCR7,ELOVL6, FASN,FDPS,HMGCR,HMGCS1,IDH1,IDI1,INSIG1, LSS,MVD,MVK,PCSK9,MSMO1,SQLE,SREBF2	ACTR2,APAF1,ARF3,ATP10B,CDCP1,CEACAM1,CEACAM5, CLIC5,CTNNA1,CTNND1,CTTNBP2NL,DHCR24,FDFT1,GPD2, HMGCR,KDM1B,LOC284441,RAB19,SLC44A4,SLCO2A1,USP38

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 DHCR24

There's no related Drug.

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Cross referenced IDs for DHCR24

* 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