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 RDH12
Basic gene info.Gene symbolRDH12
Gene nameretinol dehydrogenase 12 (all-trans/9-cis/11-cis)
SynonymsLCA13|LCA3|RP53|SDR7C2
CytomapUCSC genome browser: 14q24.1
Genomic locationchr14 :68168602-68201168
Type of geneprotein-coding
RefGenesNM_152443.2,
Ensembl idENSG00000139988
Descriptionall-trans and 9-cis retinol dehydrogenaseretinol dehydrogenase 12retinol dehydrogenase 12, all-trans and 9-cisshort chain dehydrogenase/reductase family 7C, member 2
Modification date20141219
dbXrefs MIM : 608830
HGNC : HGNC
Ensembl : ENSG00000139988
HPRD : 10585
Vega : OTTHUMG00000170032
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RDH12
BioGPS: 145226
Gene Expression Atlas: ENSG00000139988
The Human Protein Atlas: ENSG00000139988
PathwayNCI Pathway Interaction Database: RDH12
KEGG: RDH12
REACTOME: RDH12
ConsensusPathDB
Pathway Commons: RDH12
MetabolismMetaCyc: RDH12
HUMANCyc: RDH12
RegulationEnsembl's Regulation: ENSG00000139988
miRBase: chr14 :68,168,602-68,201,168
TargetScan: NM_152443
cisRED: ENSG00000139988
ContextiHOP: RDH12
cancer metabolism search in PubMed: RDH12
UCL Cancer Institute: RDH12
Assigned class in ccmGDBC

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Phenotypic Information for RDH12(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RDH12
Familial Cancer Database: RDH12
* 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: RDH12
MedGen: RDH12 (Human Medical Genetics with Condition)
ClinVar: RDH12
PhenotypeMGI: RDH12 (International Mouse Phenotyping Consortium)
PhenomicDB: RDH12

Mutations for RDH12
* 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
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 RDH12 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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=29)
Stat. for Synonymous SNVs
(# total SNVs=10)
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
chr14:68193795-68193795p.K182N5
chr14:68200555-68200555p.R314Q4
chr14:68191872-68191872p.E82K3
chr14:68200490-68200490p.P292P2
chr14:68200517-68200517p.E301E2
chr14:68195964-68195964p.R239W2
chr14:68191259-68191259p.G46G2
chr14:68193731-68193731p.R161Q2
chr14:68192765-68192765p.?2
chr14:68191292-68191292p.R57S1

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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
# sample11 7  3  1 121  51 5
# mutation11 6  3  1 121  51 5
nonsynonymous SNV 1 5  3     21  21 4
synonymous SNV1  1     1 1    3  1
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
chr14:68200555p.R314Q3
chr14:68191259p.G46G2
chr14:68191904p.M130T1
chr14:68196080p.S10F1
chr14:68189388p.G145R1
chr14:68191929p.F25L1
chr14:68200518p.L154I1
chr14:68191196p.S174S1
chr14:68192797p.T49M1
chr14:68200554p.F251F1

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 RDH12 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 RDH12

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

AADACL2,ACER1,C1orf105,CARD18,CYP2F1,CYP3A4,DGAT2,
FGF22,KPRP,KRT78,KRT79,KRTDAP,LCE1A,LCE1F,
LCE2A,LIPM,NKPD1,PLA2G2F,PNPLA1,PSAPL1,RDH12
ACP5,SOWAHD,CALM3,CPLX4,CRNN,CTSD,CYP2S1,
DEFB126,GM2A,GPR32,GRN,IL17C,MICAL1,PSG9,
PTCRA,RDH12,SCGB2A1,SERPINB11,SIGLEC7,SLC29A3,SNORA25

APIP,BARHL2,NPAP1,LINC00336,CD177,CYP3A43,FABP1,
GLRA2,MYL1,NAT2,OR4K15,OR52N5,PGLYRP4,PWRN1,
RASL11A,RDH12,REN,SLC4A10,SPSB4,SULT6B1,USP2
ALOX12,C10orf113,CCDC173,CCDC70,CSAG2,DEFA1B,DMP1,
FAM47A,FKSG83,GKN1,HBM,IL1RAPL1,KRT3,LOC100128023,
OR52N1,PATE3,PYCR2,RDH12,TBC1D28,TRMT61A,TTTY9B
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 RDH12
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 12 (all-trans/9-cis/11-cis)approved; nutraceuticalVitamin A


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Cross referenced IDs for RDH12
* 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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