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 CH25H
Basic gene info.Gene symbolCH25H
Gene namecholesterol 25-hydroxylase
SynonymsC25H
CytomapUCSC genome browser: 10q23
Genomic locationchr10 :90965693-90967071
Type of geneprotein-coding
RefGenesNM_003956.3,
Ensembl idENSG00000138135
Descriptioncholesterol 25-monooxygenaseh25OH
Modification date20141207
dbXrefs MIM : 604551
HGNC : HGNC
Ensembl : ENSG00000138135
HPRD : 05183
Vega : OTTHUMG00000018705
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CH25H
BioGPS: 9023
Gene Expression Atlas: ENSG00000138135
The Human Protein Atlas: ENSG00000138135
PathwayNCI Pathway Interaction Database: CH25H
KEGG: CH25H
REACTOME: CH25H
ConsensusPathDB
Pathway Commons: CH25H
MetabolismMetaCyc: CH25H
HUMANCyc: CH25H
RegulationEnsembl's Regulation: ENSG00000138135
miRBase: chr10 :90,965,693-90,967,071
TargetScan: NM_003956
cisRED: ENSG00000138135
ContextiHOP: CH25H
cancer metabolism search in PubMed: CH25H
UCL Cancer Institute: CH25H
Assigned class in ccmGDBC

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Phenotypic Information for CH25H(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CH25H
Familial Cancer Database: CH25H
* 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: CH25H
MedGen: CH25H (Human Medical Genetics with Condition)
ClinVar: CH25H
PhenotypeMGI: CH25H (International Mouse Phenotyping Consortium)
PhenomicDB: CH25H

Mutations for CH25H
* 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 CH25H related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=12)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr10:90966402-90966402p.S216S2
chr10:90966983-90966983p.L23F1
chr10:90966300-90966300p.F250F1
chr10:90966611-90966611p.H147N1
chr10:90966990-90966990p.L20L1
chr10:90966332-90966332p.D240N1
chr10:90966633-90966633p.F139L1
chr10:90966996-90966996p.L18L1
chr10:90966377-90966377p.H225Y1
chr10:90966639-90966639p.M137I1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample11 6    2  51   23 3
# mutation11 5    2  51   33 3
nonsynonymous SNV11 4    1  51   22  
synonymous SNV   2    1       11 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
chr10:90966295p.P252L2
chr10:90967020p.T171T1
chr10:90966300p.L20L1
chr10:90966723p.A168V1
chr10:90966469p.Q10H1
chr10:90966727p.K148K1
chr10:90966472p.H147N1
chr10:90966740p.F139F1
chr10:90966519p.M137I1
chr10:90966765p.P115H1

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 CH25H 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 CH25H

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

ARHGEF15,MEDAG,CCL2,CH25H,CSRNP1,ACKR1,DUSP1,
EMCN,ETS2,GRASP,HBEGF,IL6,LOC100302650,MCTP1,
MFAP4,S1PR1,SELP,SOCS3,SOX7,SPRY1,ZFP36
ADAMTS1,AGR2___C11orf96,ATF3,C2CD4B,CCL2,CCL3,CCL4,
CD83,CDKN1A,CH25H,IL1B,IL6,NR4A1,NR4A2,
OSM,RGS16,RND1,SELE,SLC2A3,SOCS3,ZFP36

CH25H,COL9A1,CYGB,EDNRB,ELN,FAT4,FOXF1,
FOXF2,FZD8,GLI1,GPBAR1,ISLR2,LRRN4CL,LRRTM2,
LSAMP,NKX2-3,PCDH18,PDZD2,TCF21,WBSCR17,WNT2B
AREG,BHLHE40,CCL3,CCL4L2,CH25H,DUSP2,EGR1,
HBEGF,IER2,IER3,IL1A,IL1B,JUNB,MAFF,
NR4A1,NR4A2,PHLDA1,PLK3,SIK1,SLC2A3,ZNF165
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 CH25H


There's no related Drug.
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Cross referenced IDs for CH25H
* 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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