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 RDH10
Basic gene info.Gene symbolRDH10
Gene nameretinol dehydrogenase 10 (all-trans)
SynonymsSDR16C4
CytomapUCSC genome browser: 8q21.11
Genomic locationchr8 :74206836-74237520
Type of geneprotein-coding
RefGenesNM_172037.4,
Ensembl idENSG00000121039
Descriptionretinol dehydrogenase 10short chain dehydrogenase/reductase family 16C, member 4
Modification date20141207
dbXrefs MIM : 607599
HGNC : HGNC
Ensembl : ENSG00000121039
HPRD : 07605
Vega : OTTHUMG00000164492
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RDH10
BioGPS: 157506
Gene Expression Atlas: ENSG00000121039
The Human Protein Atlas: ENSG00000121039
PathwayNCI Pathway Interaction Database: RDH10
KEGG: RDH10
REACTOME: RDH10
ConsensusPathDB
Pathway Commons: RDH10
MetabolismMetaCyc: RDH10
HUMANCyc: RDH10
RegulationEnsembl's Regulation: ENSG00000121039
miRBase: chr8 :74,206,836-74,237,520
TargetScan: NM_172037
cisRED: ENSG00000121039
ContextiHOP: RDH10
cancer metabolism search in PubMed: RDH10
UCL Cancer Institute: RDH10
Assigned class in ccmGDBC

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Phenotypic Information for RDH10(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RDH10
Familial Cancer Database: RDH10
* 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: RDH10
MedGen: RDH10 (Human Medical Genetics with Condition)
ClinVar: RDH10
PhenotypeMGI: RDH10 (International Mouse Phenotyping Consortium)
PhenomicDB: RDH10

Mutations for RDH10
* 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 RDH10 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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample2  2    1     1 1
GAIN (# sample)2  2    1     1 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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=25)
Stat. for Synonymous SNVs
(# total SNVs=7)
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
chr8:74235228-74235228p.R328K2
chr8:74235028-74235028p.I295I2
chr8:74231354-74231354p.T183T2
chr8:74233246-74233246p.G235A2
chr8:74231418-74231418p.A205S1
chr8:74234910-74234911p.?1
chr8:74209570-74209570p.N144I1
chr8:74235200-74235200p.K319E1
chr8:74231424-74231424p.V207I1
chr8:74207551-74207551p.V9V1

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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
# sample3  4       22   4114
# mutation3  4       22   4116
nonsynonymous SNV3  3       22   2114
synonymous SNV   1            2  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
chr8:74231354p.T183T2
chr8:74235043p.S198S1
chr8:74231399p.A205S1
chr8:74235196p.C211R1
chr8:74209448p.E227K1
chr8:74231418p.K229R1
chr8:74235200p.M286V1
chr8:74209455p.E103D1
chr8:74233173p.R291L1
chr8:74209456p.P106S1

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 RDH10 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 RDH10

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

AK2,CEACAM19,CHRAC1,FAM71C,FAM72D,IFNA4,IQCF5,
KIAA1804,NCK1,NDRG1,PDE7A,POP1,PTDSS1,RARRES1,
RDH10,SLC25A32,SLC6A15,TAAR1,TAAR8,TMEM123,ZNF695
ABHD5,ACACB,ACSS3,ACVR1C,ADH1B,ADRBK2,AZI2,
BNIP3L,CDO1,GHR,HOXB8,IGF1,LOC283392,OXCT1,
PECR,PTEN,PTENP1,RDH10,RHOBTB3,SLC19A3,SLC22A3

ASPH,CA8,EEF1DP3,FAM84B,FAM91A1,FLJ30679,FOXD1,
GFI1B,HNF4G,IMPAD1,JPH1,MAL2,MTDH,MTFR1,
PTDSS1,RDH10,SNX16,TCEA1,TERF1,TPD52,VCPIP1
SOWAHA,CYP2B6,CYP2C18,FLVCR1,GBA3,GIPC2,GLS,
HNF4G,ING2,MACC1,MEP1A,MYO1A,NR1H4,PGRMC1,
PLIN2,RDH10,SLC17A8,SLC1A1,SLC23A3,SLC3A1,TTC38
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 RDH10


There's no related Drug.
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Cross referenced IDs for RDH10
* 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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