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 RDH8
Basic gene info.Gene symbolRDH8
Gene nameretinol dehydrogenase 8 (all-trans)
SynonymsPRRDH|SDR28C2
CytomapUCSC genome browser: 19p13.2
Genomic locationchr19 :10123924-10132954
Type of geneprotein-coding
RefGenesNM_015725.2,
Ensembl idENSG00000080511
Descriptionphotoreceptor outer segment all-trans retinol dehydrogenaseretinol dehydrogenase 8short chain dehydrogenase/reductase family 28C, member 2
Modification date20141207
dbXrefs MIM : 608575
HGNC : HGNC
Ensembl : ENSG00000080511
HPRD : 16350
Vega : OTTHUMG00000180392
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RDH8
BioGPS: 50700
Gene Expression Atlas: ENSG00000080511
The Human Protein Atlas: ENSG00000080511
PathwayNCI Pathway Interaction Database: RDH8
KEGG: RDH8
REACTOME: RDH8
ConsensusPathDB
Pathway Commons: RDH8
MetabolismMetaCyc: RDH8
HUMANCyc: RDH8
RegulationEnsembl's Regulation: ENSG00000080511
miRBase: chr19 :10,123,924-10,132,954
TargetScan: NM_015725
cisRED: ENSG00000080511
ContextiHOP: RDH8
cancer metabolism search in PubMed: RDH8
UCL Cancer Institute: RDH8
Assigned class in ccmGDBC

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Phenotypic Information for RDH8(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RDH8
Familial Cancer Database: RDH8
* 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_RETINOL_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: RDH8
MedGen: RDH8 (Human Medical Genetics with Condition)
ClinVar: RDH8
PhenotypeMGI: RDH8 (International Mouse Phenotyping Consortium)
PhenomicDB: RDH8

Mutations for RDH8
* 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
pancreasRDH8chr191013151110131531chr192090881620908836
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 RDH8 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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=44)
Stat. for Synonymous SNVs
(# total SNVs=13)
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
chr19:10129572-10129572p.V143A2
chr19:10132297-10132297p.V270M2
chr19:10131987-10131987p.A198V2
chr19:10124205-10124205p.S11F2
chr19:10131441-10131441p.E167K2
chr19:10132083-10132083p.S230F2
chr19:10132280-10132280p.L264R2
chr19:10132286-10132286p.T266M2
chr19:10132290-10132290p.L267L1
chr19:10127741-10127741p.T38A1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   82 5  1 854 298 11
# mutation   81 5  1 854 2107 11
nonsynonymous SNV   61 1    743 276 9
synonymous SNV   2  4  1 111  31 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])

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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
chr19:10132297p.T286M2
chr19:10124205p.S31Y2
chr19:10131987p.V290M2
chr19:10132286p.A218V2
chr19:10131387p.L319M1
chr19:10132415p.S92L1
chr19:10127775p.S162I1
chr19:10132058p.S250S1
chr19:10129427p.T326K1
chr19:10132293p.C96C1

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 RDH8 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 RDH8

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

ADAMTS14,ARSI,BMP1,COL5A3,DMRTB1,DPEP3,EGFL6,
FEZ1,HTR7,INSM2,KCNJ15,LINC00626,MMP13,OR10R2,
PPEF1,RDH8,RFX8,SFTA1P,SLC2A7,TDO2,THY1
AIFM2,ALDOC,ASAH1,FAM213A,HOGA1,EPB42,EPHX1,
GLYAT,GPAM,SLC25A51,NMT2,PCBP3,POLN,PPP2R1B,
PYGL,RDH8,RFTN1,SAR1A,SEPT11,SPATA9,TSPAN3

ATP12A,C3P1,CAP1,ACKR2___ACKR4,CD7,DIO1,FLJ35024,
GSTA3,HOXC12,KCNB2,KLRG2,LOC100133669,MS4A15,RDH8,
RRAGC,S100A7A,SLC30A2,STOML3,TESK2,VGLL1,VSIG10L
C11orf40,COLCA2,AXDND1,EQTN,CA6,FAM58BP,HHLA1,
HORMAD2,LOC157381,OR10A2,OR11H12,OR1B1,OR2AK2,FOXN3-AS2,
RDH8,SNORA54,SNORA5B,SPINK9,SSX3,TAS2R41,WFDC13
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 RDH8
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
DB00162retinol dehydrogenase 8 (all-trans)approved; nutraceuticalVitamin A


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Cross referenced IDs for RDH8
* 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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