Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 symbol	RDH12
	Gene name	retinol dehydrogenase 12 (all-trans/9-cis/11-cis)
	Synonyms	LCA13\|LCA3\|RP53\|SDR7C2
	Cytomap	UCSC genome browser: 14q24.1
	Genomic location	chr14 :68168602-68201168
	Type of gene	protein-coding
	RefGenes	NM_152443.2,
	Ensembl id	ENSG00000139988
	Description	all-trans and 9-cis retinol dehydrogenaseretinol dehydrogenase 12retinol dehydrogenase 12, all-trans and 9-cisshort chain dehydrogenase/reductase family 7C, member 2
	Modification date	20141219
dbXrefs	MIM : 608830
	HGNC : HGNC
	Ensembl : ENSG00000139988
	HPRD : 10585
	Vega : OTTHUMG00000170032
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RDH12
	BioGPS: 145226
	Gene Expression Atlas: ENSG00000139988
	The Human Protein Atlas: ENSG00000139988
Pathway	NCI Pathway Interaction Database: RDH12
	KEGG: RDH12
	REACTOME: RDH12
	ConsensusPathDB
	Pathway Commons: RDH12
Metabolism	MetaCyc: RDH12
	HUMANCyc: RDH12
Regulation	Ensembl's Regulation: ENSG00000139988
	miRBase: chr14 :68,168,602-68,201,168
	TargetScan: NM_152443
	cisRED: ENSG00000139988
Context	iHOP: RDH12
	cancer metabolism search in PubMed: RDH12
	UCL Cancer Institute: RDH12
Assigned class in ccmGDB	C

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Phenotypic Information for RDH12(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
KEGG_RETINOL_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: RDH12
	MedGen: RDH12 (Human Medical Genetics with Condition)
	ClinVar: RDH12
Phenotype	MGI: RDH12 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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.

Sample

Symbol_a

Chr_a

Start_a

End_a

Symbol_b

Chr_b

Start_b

End_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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows RDH12 related fusion information.

Head Gene

Tail Gene

Accession

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy 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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr14:68193795-68193795	p.K182N	5
chr14:68200555-68200555	p.R314Q	4
chr14:68191872-68191872	p.E82K	3
chr14:68195964-68195964	p.R239W	2
chr14:68191259-68191259	p.G46G	2
chr14:68193731-68193731	p.R161Q	2
chr14:68192765-68192765	p.?	2
chr14:68200490-68200490	p.P292P	2
chr14:68200517-68200517	p.E301E	2
chr14:68191306-68191306	p.R62Q	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1	1		7			3			1		1	2	1			5	1		5
# mutation	1	1		6			3			1		1	2	1			5	1		5
nonsynonymous SNV		1		5			3						2	1			2	1		4
synonymous SNV	1			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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr14:68200555	p.R314Q	3
chr14:68191259	p.G46G	2
chr14:68192797	p.F25L	1
chr14:68200554	p.L154I	1
chr14:68192801	p.S174S	1
chr14:68191267	p.T49M	1
chr14:68192802	p.F251F	1
chr14:68191275	p.G52C	1
chr14:68192813	p.L277V	1
chr14:68191281	p.E54K	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00162	retinol dehydrogenase 12 (all-trans/9-cis/11-cis)	approved; nutraceutical	Vitamin 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