Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 CHDH
Basic gene info.Gene symbolCHDH
Gene namecholine dehydrogenase
Synonyms-
CytomapUCSC genome browser: 3p21.1
Genomic locationchr3 :53850323-53880420
Type of geneprotein-coding
RefGenesNM_018397.4,
Ensembl idENSG00000016391
DescriptionCDHCHDcholine dehydrogenase, mitochondrial
Modification date20141207
dbXrefs HGNC : HGNC
HPRD : 13050
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CHDH
BioGPS: 55349
Gene Expression Atlas: ENSG00000016391
The Human Protein Atlas: ENSG00000016391
PathwayNCI Pathway Interaction Database: CHDH
KEGG: CHDH
REACTOME: CHDH
ConsensusPathDB
Pathway Commons: CHDH
MetabolismMetaCyc: CHDH
HUMANCyc: CHDH
RegulationEnsembl's Regulation: ENSG00000016391
miRBase: chr3 :53,850,323-53,880,420
TargetScan: NM_018397
cisRED: ENSG00000016391
ContextiHOP: CHDH
cancer metabolism search in PubMed: CHDH
UCL Cancer Institute: CHDH
Assigned class in ccmGDBC

Top
Phenotypic Information for CHDH(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CHDH
Familial Cancer Database: CHDH
* 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
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM

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

Mutations for CHDH
* 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 CHDH related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF930030ARPC2202812219099129219100136CHDH27659135385094953851264

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

Top
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.

Top
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=6

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=26)
Stat. for Synonymous SNVs
(# total SNVs=18)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

Top
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
chr3:53857676-53857676p.L120L6
chr3:53857673-53857673p.Y121Y3
chr3:53857803-53857803p.L78R3
chr3:53857356-53857356p.W227*2
chr3:53856621-53856621p.R251H2
chr3:53853588-53853588p.R412W2
chr3:53851900-53851900p.I563I2
chr3:53851977-53851977p.E538K1
chr3:53856520-53856520p.R285G1
chr3:53852202-53852202p.R463C1

Top
check002.gifSNV 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 ID1234567891011121314151617181920
# sample  1101 2 31 121  67 3
# mutation  1101 2 31 131  68 4
nonsynonymous SNV  17  2 21 11   44 2
synonymous SNV   31   1   21  24 2
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
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
chr3:53851900p.I563I2
chr3:53851977p.R503W1
chr3:53857556p.G320V1
chr3:53853588p.A500A1
chr3:53855757p.L319L1
chr3:53852023p.S490S1
chr3:53857751p.S301Y1
chr3:53853612p.E456K1
chr3:53856520p.R285G1
chr3:53852036p.R271C1

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 CHDH 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 CHDH

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))
Top
check002.gifCNV 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
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

ACTR8,APPL1,BCDIN3D,C3orf18,CHDH,FLNB,HEMK1,
IL17RB,IP6K1,LRIG1,LZTFL1,MAGI1,NICN1,NISCH,
RABEP1,RNF123,TNK1,USP19,VPRBP,WDR6,ZBTB4
BBS1,CASZ1,CCDC120,CDK20,CHDH,DFNB31,DLG3,
ESRP2,GRHL2,HKR1,HMGXB3,KIAA1522,LIMK2,LOC100130093,
MARK2,OVOL2,PLEKHA6,PSD4,SEMA4B,SHROOM3,SIPA1L3

BAP1,CACNA1D,CHDH,DAGLA,ERBB3,IL17RB,LIMD1,
LOC652276,LRRC2,MYRIP,PDPK1,PLXNB1,RAB40C,RBM15B,
SCAP,SHANK2,SMARCC1,SPATA2,ST6GAL1,TGIF2,TMEM63A
ARSE,BCL2L14,C11orf52,RRNAD1,RBBP8NL,CACNA2D4,CHDH,
COX19,FMO5,GATA6,HNF1A,LOC389332,MNX1,PCBP2,
PCK1,PGAP2,PPFIBP2,ARHGEF28,RORC,SLC39A11,SMPDL3B
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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for CHDH


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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas