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 DHCR7
Basic gene info.Gene symbolDHCR7
Gene name7-dehydrocholesterol reductase
SynonymsSLOS
CytomapUCSC genome browser: 11q13.4
Genomic locationchr11 :71145456-71159477
Type of geneprotein-coding
RefGenesNM_001163817.1,
NM_001360.2,
Ensembl idENSG00000172893
Description7-DHC reductasedelta-7-dehydrocholesterol reductaseputative sterol reductase SR-2sterol delta-7-reductase
Modification date20141219
dbXrefs MIM : 602858
HGNC : HGNC
Ensembl : ENSG00000172893
HPRD : 04174
Vega : OTTHUMG00000167346
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DHCR7
BioGPS: 1717
Gene Expression Atlas: ENSG00000172893
The Human Protein Atlas: ENSG00000172893
PathwayNCI Pathway Interaction Database: DHCR7
KEGG: DHCR7
REACTOME: DHCR7
ConsensusPathDB
Pathway Commons: DHCR7
MetabolismMetaCyc: DHCR7
HUMANCyc: DHCR7
RegulationEnsembl's Regulation: ENSG00000172893
miRBase: chr11 :71,145,456-71,159,477
TargetScan: NM_001163817
cisRED: ENSG00000172893
ContextiHOP: DHCR7
cancer metabolism search in PubMed: DHCR7
UCL Cancer Institute: DHCR7
Assigned class in ccmGDBC

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Phenotypic Information for DHCR7(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: DHCR7
Familial Cancer Database: DHCR7
* 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: DHCR7
MedGen: DHCR7 (Human Medical Genetics with Condition)
ClinVar: DHCR7
PhenotypeMGI: DHCR7 (International Mouse Phenotyping Consortium)
PhenomicDB: DHCR7

Mutations for DHCR7
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows DHCR7 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BI038607DENND4B262941153915197153915466DHCR7289372117114600571146088
CR741097DHCR766101117114584071145875DHCR795178117114576971145852

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1                
GAIN (# sample)1                
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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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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=32)
Stat. for Synonymous SNVs
(# total SNVs=28)
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
chr11:71150111-71150111p.F215L5
chr11:71155948-71155948p.G17G4
chr11:71148915-71148915p.F302F3
chr11:71152464-71152464p.I145I2
chr11:71149970-71149970p.L262L2
chr11:71155106-71155106p.I85S2
chr11:71150017-71150017p.A247T2
chr11:71146691-71146691p.D386D2
chr11:71152376-71152376p.D175Y2
chr11:71146749-71146749p.R367H2

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample12 61 2 2  641  154 10
# mutation12 61 2 2  551  164 10
nonsynonymous SNV   41 1 2  331  103 2
synonymous SNV12 2  1    22   61 8
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
chr11:71150111p.F215L,DHCR75
chr11:71150017p.F302F,DHCR73
chr11:71148915p.A247P,DHCR73
chr11:71152365p.A206T,DHCR72
chr11:71152464p.I178I,DHCR72
chr11:71152283p.G17G,DHCR72
chr11:71155948p.I145I,DHCR72
chr11:71155984p.T93T,DHCR71
chr11:71148959p.R367H,DHCR71
chr11:71152330p.P203L,DHCR71

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 DHCR7 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 DHCR7

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

ALG3,C11orf24,KNSTRN,CMC2,CCNB2,CENPN,CHKA,
CLPB,CTTN,DHCR7,FADD,FDPS,IDI1,KARS,
NADSYN1,PHF5A,DESI1,RANBP1,MSMO1,SLC43A3,WDR3
AACS,ACSL3,ADAM2,AFMID,ALOX15B,B3GAT1,DHCR7,
DHRS2,GGT1,GGTLC2,MPV17L,MVD,MVK,NSUN2,
PNLIPRP3,MSMO1,SERHL2,SERHL,SLC15A1,SRD5A1,TARP

ACAT2,ALDOC,C6orf223,CYP51A1,DHCR24,DHCR7,FASN,
HMGCR,HMGCS1,INSIG1,LSS,MVD,MVK,OVOL1,
PCSK9,PPME1,MSMO1,SC5D,SCD,SLC29A2,SQLE
ACSL3,AP2B1,C14orf1,C6orf223,CYP51A1,DHCR7,FASN,
FGFBP1,HMGCS1,INSIG1,KIAA1244,LSS,MUC4,MUC5B,
MVD,MVK,NSDHL,PCSK9,PDE11A,MSMO1,SQLE
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 DHCR7
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB001577-dehydrocholesterol reductaseapproved; nutraceuticalNADH


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Cross referenced IDs for DHCR7
* 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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