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 RDH16
Basic gene info.Gene symbolRDH16
Gene nameretinol dehydrogenase 16 (all-trans)
SynonymsRODH-4|SDR9C8
CytomapUCSC genome browser: 12q13.3
Genomic locationchr12 :57345215-57351418
Type of geneprotein-coding
RefGenesNM_003708.3,
Ensembl idENSG00000139547
Descriptionmicrosomal NAD(+)-dependent retinol dehydrogenase 4microsomal NAD+-dependent retinol dehydrogenase 4retinol dehydrogenase 16retinol dehydrogenase 16 (all-trans and 13-cis)short chain dehydrogenase/reductase family 9C, member 8sterol/retinol dehydroge
Modification date20141207
dbXrefs HGNC : HGNC
HPRD : 10208
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RDH16
BioGPS: 8608
Gene Expression Atlas: ENSG00000139547
The Human Protein Atlas: ENSG00000139547
PathwayNCI Pathway Interaction Database: RDH16
KEGG: RDH16
REACTOME: RDH16
ConsensusPathDB
Pathway Commons: RDH16
MetabolismMetaCyc: RDH16
HUMANCyc: RDH16
RegulationEnsembl's Regulation: ENSG00000139547
miRBase: chr12 :57,345,215-57,351,418
TargetScan: NM_003708
cisRED: ENSG00000139547
ContextiHOP: RDH16
cancer metabolism search in PubMed: RDH16
UCL Cancer Institute: RDH16
Assigned class in ccmGDBC

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Phenotypic Information for RDH16(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RDH16
Familial Cancer Database: RDH16
* 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: RDH16
MedGen: RDH16 (Human Medical Genetics with Condition)
ClinVar: RDH16
PhenotypeMGI: RDH16 (International Mouse Phenotyping Consortium)
PhenomicDB: RDH16

Mutations for RDH16
* 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 RDH16 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 # sample 1           1   
GAIN (# sample) 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=26)
Stat. for Synonymous SNVs
(# total SNVs=10)
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
chr12:57346638-57346638p.A237T2
chr12:57345981-57345981p.S262S2
chr12:57346753-57346753p.G198G2
chr12:57346757-57346757p.F197C2
chr12:57348915-57348915p.S116F2
chr12:57346020-57346020p.S249S1
chr12:57351176-57351176p.L24P1
chr12:57348692-57348692p.L190L1
chr12:57345911-57345911p.D286N1
chr12:57351007-57351007p.V80V1

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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 2 7  3 2  43   82 3
# mutation 2 7  3 2  43   82 3
nonsynonymous SNV 1 5    1  11   32 3
synonymous SNV 1 2  3 1  32   5   
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
chr12:57348692p.S262S2
chr12:57345981p.S116F2
chr12:57348915p.G198G2
chr12:57346753p.L190L2
chr12:57351084p.V264M1
chr12:57345952p.P121S1
chr12:57348713p.C257Y1
chr12:57351117p.D83N1
chr12:57345977p.S249S1
chr12:57348759p.E63K1

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 RDH16 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 RDH16

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

AOC1,BRDT,BST2,BTNL8,C10orf82,CACNG1,FLJ45983,
GKN1,GOT1L1,GRINA,HEBP1,HTR7P1,KIAA1467,LSM1,
MFSD3,PCSK2,PRR13,PVALB,RDH16,SNHG6,TWIST1
ASCL2,C11orf85,THEM6,CNTD2,FAM110A,GATA5,GDPD3,
HSD17B1,KCNF1,KREMEN2,MAPK8IP2,MYT1,OR56A3,POLR3K,
PSCA,PYY,RDH16,SLC7A13,VSTM2A,ABHD11-AS1,WNT3A

ALDOB,CALML5,CCDC140,CNFN,DCAF4L1,FAM71F1,FAM71F2,
FMO6P,GP6,GPR149,KRTAP10-12,LOC339568,LOC340508,OBP2A,
OBP2B,POLN,RASGRF1,RDH16,SRD5A2,TFAP2A,ZAN
TEX29,CFAP69,CCDC73,CDC42EP3,CHODL,CIDECP,F2,
HPD,LCE1C,LOC222699,LOC387647,MOAP1,PAGE4,PAH,
RDH16,RHOXF1,SUN3,TAS2R20,USP25,VEZF1,ZNF528
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 RDH16


There's no related Drug.
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Cross referenced IDs for RDH16
* 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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