Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolDHCR24
Gene name24-dehydrocholesterol reductase
SynonymsDCE|Nbla03646|SELADIN1|seladin-1
CytomapUCSC genome browser: 1p32.3
Genomic locationchr1 :55315299-55352921
Type of geneprotein-coding
RefGenesNM_014762.3,
Ensembl idENSG00000116133
Description3 beta-hydroxysterol delta 24-reductase3-beta-hydroxysterol delta-24-reductasedelta(24)-sterol reductasedesmosterol-to-cholesterol enzymediminuto/dwarf1 homologseladin 1selective AD indicator 1
Modification date20141207
dbXrefs MIM : 606418
HGNC : HGNC
Ensembl : ENSG00000116133
HPRD : 05916
Vega : OTTHUMG00000009989
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DHCR24
BioGPS: 1718
Gene Expression Atlas: ENSG00000116133
The Human Protein Atlas: ENSG00000116133
PathwayNCI Pathway Interaction Database: DHCR24
KEGG: DHCR24
REACTOME: DHCR24
ConsensusPathDB
Pathway Commons: DHCR24
MetabolismMetaCyc: DHCR24
HUMANCyc: DHCR24
RegulationEnsembl's Regulation: ENSG00000116133
miRBase: chr1 :55,315,299-55,352,921
TargetScan: NM_014762
cisRED: ENSG00000116133
ContextiHOP: DHCR24
cancer metabolism search in PubMed: DHCR24
UCL Cancer Institute: DHCR24
Assigned class in ccmGDBC

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Phenotypic Information for DHCR24(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: DHCR24
MedGen: DHCR24 (Human Medical Genetics with Condition)
ClinVar: DHCR24
PhenotypeMGI: DHCR24 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
prostateDHCR24chr15533164755331647OPTCchr1203467515203467515
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows DHCR24 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE828048CNPPD132742220036940220037211DHCR2426538015531531455315429
DB244252GAS51781173833503173833579DHCR247456015531635355316839
DA340395LOC1005074121174?115720115893DHCR2417456915534939355352903
DA046822FAM105A118851461038214610569DHCR2418973815531701455317563
AA658920DHCR24814615531612955316267DHCR2414452715531626355316646
AW997410DHCR24113515531915055319284QSOX21271479139118628139118648
BF918420ZNF2761486168980661589806687DHCR248239415531639255316704
AI207637DHCR24153315531650355317035B4GALT5518631204825218348252296
AW997408DHCR24512615531916255319284QSOX21181389139118628139118648
AI369276USP221283172090304820903330DHCR2427937515535228955352385

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy 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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr1:55319719-55319719p.N403N3
chr1:55337094-55337094p.G269R2
chr1:55341714-55341714p.R132C2
chr1:55352725-55352725p.L23Q2
chr1:55337260-55337260p.A213A2
chr1:55317925-55317925p.C511Y1
chr1:55341662-55341662p.I149T1
chr1:55319767-55319767p.M387I1
chr1:55349446-55349446p.V78L1
chr1:55317941-55317941p.V506L1

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample2412       2 1  25 5
# mutation3412       2 1  25 8
nonsynonymous SNV2312       2 1  13 5
synonymous SNV11              12 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr1:55317925p.C511Y1
chr1:55352654p.E309D1
chr1:55319845p.D47N1
chr1:55337221p.S488F1
chr1:55317994p.H307H1
chr1:55319868p.R478Q1
chr1:55337260p.L293L1
chr1:55318024p.V464M1
chr1:55331007p.Q262R1
chr1:55340771p.D436N1

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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



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