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 OGDHL
Basic gene info.Gene symbolOGDHL
Gene nameoxoglutarate dehydrogenase-like
Synonyms-
CytomapUCSC genome browser: 10q11.23
Genomic locationchr10 :50942686-50970425
Type of geneprotein-coding
RefGenesNM_001143996.1,
NM_001143997.1,NM_018245.2,
Ensembl idENSG00000197444
Description2-oxoglutarate dehydrogenase complex component E1-like2-oxoglutarate dehydrogenase-like, mitochondrialOGDC-E1-likealpha-ketoglutarate dehydrogenase-like
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000197444
HPRD : 07704
Vega : OTTHUMG00000018200
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_OGDHL
BioGPS: 55753
Gene Expression Atlas: ENSG00000197444
The Human Protein Atlas: ENSG00000197444
PathwayNCI Pathway Interaction Database: OGDHL
KEGG: OGDHL
REACTOME: OGDHL
ConsensusPathDB
Pathway Commons: OGDHL
MetabolismMetaCyc: OGDHL
HUMANCyc: OGDHL
RegulationEnsembl's Regulation: ENSG00000197444
miRBase: chr10 :50,942,686-50,970,425
TargetScan: NM_001143996
cisRED: ENSG00000197444
ContextiHOP: OGDHL
cancer metabolism search in PubMed: OGDHL
UCL Cancer Institute: OGDHL
Assigned class in ccmGDBC

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

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

Mutations for OGDHL
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
breastOGDHLchr105095726050957260NDUFC2-KCTD14chr117776043577760435
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 OGDHL related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BP348542OGDHL1392105094293650970356OGDHL388581105096491550966550

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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=127)
Stat. for Synonymous SNVs
(# total SNVs=32)
Stat. for Deletions
(# total SNVs=2)
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
chr10:50954894-50954894p.A400T6
chr10:50966551-50966551p.R30C4
chr10:50959882-50959882p.R247H3
chr10:50964886-50964886p.R104Q3
chr10:50944482-50944482p.G892E2
chr10:50954898-50954898p.D398D2
chr10:50955203-50955203p.R347C2
chr10:50947856-50947856p.P724S2
chr10:50955213-50955213p.E343E2
chr10:50954813-50954813p.V427I2

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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
# sample651173 9 2 124112113811216
# mutation651193 9 2 125112114813221
nonsynonymous SNV441143 8 2  175 1 367217
synonymous SNV21 5  1   1862 1126 4
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
chr10:50954894p.A191T,OGDHL4
chr10:50966551p.R30C,OGDHL3
chr10:50952143p.S365F,OGDHL2
chr10:50946288p.K355N,OGDHL2
chr10:50952707p.E700K,OGDHL2
chr10:50955201p.A571A,OGDHL2
chr10:50952736p.R138R,OGDHL2
chr10:50944432p.V219V,OGDHL2
chr10:50954808p.R38H,OGDHL2
chr10:50959882p.V218I,OGDHL2

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 OGDHL 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 OGDHL

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

ACTL6B,AP3B2,APLP1,CRMP1,AMER3,GNG4,KCNH2,
UNC79,OGDHL,PCSK1,PHF21B,PSD,PTPRN,RUNDC3A,
SCG3,SNAP25,SYN1,SYP,SYT4,TMEM145,UNC13A
ABCB9,ASCL2,C11orf85,C2orf50,C2orf54,RHPN1-AS1,THEM6,
CALML5,CPA6,RIPPLY3,ENTPD8,FAM110A,KLHL35,MAPK8IP2,
MCHR1,OGDHL,PCSK1N,PYCRL,TRIB3,ABHD11-AS1,WNT3A

CHRNA2,DLX6AS,ERP27,GPR83,GPR98,KCTD16,KNG1,
KRT36,KRT38,LCN10,MYL3,NAV2,OGDHL,TGM5,
TMPRSS6,UGT2A3,UGT2B7,UNC13C,USH1G,VSTM2B,ZNF660
AEBP1,AFAP1L2,ARHGAP20,BMX,CHAT,CORO2B,EMX2,
EMX2OS,GSPT2,HOXD3,HOXD8,HTR3E,KLK13,MAN1C1,
MEGF9,MFGE8,OGDHL,PCDHGA9,SH2D7,TMEM150C,TSPYL1
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 OGDHL


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