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 RDH8

Basic gene info.	Gene symbol	RDH8
	Gene name	retinol dehydrogenase 8 (all-trans)
	Synonyms	PRRDH\|SDR28C2
	Cytomap	UCSC genome browser: 19p13.2
	Genomic location	chr19 :10123924-10132954
	Type of gene	protein-coding
	RefGenes	NM_015725.2,
	Ensembl id	ENSG00000080511
	Description	photoreceptor outer segment all-trans retinol dehydrogenaseretinol dehydrogenase 8short chain dehydrogenase/reductase family 28C, member 2
	Modification date	20141207
dbXrefs	MIM : 608575
	HGNC : HGNC
	Ensembl : ENSG00000080511
	HPRD : 16350
	Vega : OTTHUMG00000180392
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RDH8
	BioGPS: 50700
	Gene Expression Atlas: ENSG00000080511
	The Human Protein Atlas: ENSG00000080511
Pathway	NCI Pathway Interaction Database: RDH8
	KEGG: RDH8
	REACTOME: RDH8
	ConsensusPathDB
	Pathway Commons: RDH8
Metabolism	MetaCyc: RDH8
	HUMANCyc: RDH8
Regulation	Ensembl's Regulation: ENSG00000080511
	miRBase: chr19 :10,123,924-10,132,954
	TargetScan: NM_015725
	cisRED: ENSG00000080511
Context	iHOP: RDH8
	cancer metabolism search in PubMed: RDH8
	UCL Cancer Institute: RDH8
Assigned class in ccmGDB	C

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Phenotypic Information for RDH8(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
KEGG_RETINOL_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: RDH8
	MedGen: RDH8 (Human Medical Genetics with Condition)
	ClinVar: RDH8
Phenotype	MGI: RDH8 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	RDH8	chr19	10131511	10131531		chr19	20908816	20908836

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 RDH8 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=3

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Somatic 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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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
chr19:10124205-10124205	p.S11F	2
chr19:10131441-10131441	p.E167K	2
chr19:10132083-10132083	p.S230F	2
chr19:10132280-10132280	p.L264R	2
chr19:10132286-10132286	p.T266M	2
chr19:10129572-10129572	p.V143A	2
chr19:10132297-10132297	p.V270M	2
chr19:10131987-10131987	p.A198V	2
chr19:10127775-10127775	p.E49A	1
chr19:10131999-10131999	p.M202T	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=2

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				8	2		5			1		8	5	4		2	9	8		11
# mutation				8	1		5			1		8	5	4		2	10	7		11
nonsynonymous SNV				6	1		1					7	4	3		2	7	6		9
synonymous SNV				2			4			1		1	1	1			3	1		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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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
chr19:10124205	p.T286M	2
chr19:10131987	p.S31Y	2
chr19:10132286	p.V290M	2
chr19:10132297	p.A218V	2
chr19:10127844	p.V106V	1
chr19:10132084	p.E187K	1
chr19:10129494	p.N278S	1
chr19:10132324	p.E17D	1
chr19:10124164	p.L107L	1
chr19:10131449	p.L189L	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 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

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


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

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 RDH8

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 8 (all-trans)	approved; nutraceutical	Vitamin 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