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 PDE6D

Basic gene info.	Gene symbol	PDE6D
	Gene name	phosphodiesterase 6D, cGMP-specific, rod, delta
	Synonyms	JBTS22\|PDED
	Cytomap	UCSC genome browser: 2q35-q36
	Genomic location	chr2 :232597146-232645974
	Type of gene	protein-coding
	RefGenes	NM_001291018.1, NM_002601.3,NR_110994.1,
	Ensembl id	ENSG00000156973
	Description	GMP-PDE deltaprotein p17retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
	Modification date	20141207
dbXrefs	MIM : 602676
	HGNC : HGNC
	Ensembl : ENSG00000156973
	HPRD : 04056
	Vega : OTTHUMG00000153785
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PDE6D
	BioGPS: 5147
	Gene Expression Atlas: ENSG00000156973
	The Human Protein Atlas: ENSG00000156973
Pathway	NCI Pathway Interaction Database: PDE6D
	KEGG: PDE6D
	REACTOME: PDE6D
	ConsensusPathDB
	Pathway Commons: PDE6D
Metabolism	MetaCyc: PDE6D
	HUMANCyc: PDE6D
Regulation	Ensembl's Regulation: ENSG00000156973
	miRBase: chr2 :232,597,146-232,645,974
	TargetScan: NM_001291018
	cisRED: ENSG00000156973
Context	iHOP: PDE6D
	cancer metabolism search in PubMed: PDE6D
	UCL Cancer Institute: PDE6D
Assigned class in ccmGDB	C

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Phenotypic Information for PDE6D(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PDE6D
	Familial Cancer Database: PDE6D

* 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_PURINE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: PDE6D
	MedGen: PDE6D (Human Medical Genetics with Condition)
	ClinVar: PDE6D
Phenotype	MGI: PDE6D (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PDE6D

Mutations for PDE6D

* 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
large_intestine	PDE6D	chr2	232622796	232622796		chr4	183163103	183163103
ovary	PDE6D	chr2	232611819	232611839		chr15	100299298	100299318

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 PDE6D related fusion information.

ID	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
BC004322	RHBDD2	39	1462	7	75511217	75518244	PDE6D	1461	2597	2	232597140	232645986
AJ001626	PDE6D	1	597	2	232597635	232645953	PDE6D	592	832	2	232597697	232602809
AV724446	ADAMTS4	1	322	1	161168402	161168723	PDE6D	312	465	2	232597175	232597328

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=9)	Stat. for Synonymous SNVs (# total SNVs=1)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	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
chr2:232602845-232602845	p.R48H	3
chr2:232602788-232602788	p.S67L	1
chr2:232602830-232602830	p.I53N	1
chr2:232602839-232602839	p.P50L	1
chr2:232597710-232597710	p.D135D	1
chr2:232597730-232597730	p.I129V	1
chr2:232603828-232603828	p.P41S	1
chr2:232597735-232597735	p.V127A	1
chr2:232645820-232645820	p.S2L	1
chr2:232601992-232601992	p.F92F	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				3								1					2			3
# mutation				3								1					2			2
nonsynonymous SNV				2								1					2			2
synonymous SNV				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
chr2:232602845	p.R48H,PDE6D	2
chr2:232597735	p.V127A	1
chr2:232601992	p.F92F	1
chr2:232602765	p.R75C,PDE6D	1
chr2:232602788	p.S67L,PDE6D	1
chr2:232602846	p.R48S,PDE6D	1
chr2:232603828	p.P41S,PDE6D	1
chr2:232645820	p.S2L,PDE6D	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 PDE6D 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 PDE6D

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


BCS1L,COPS7B,COX7B,DGUOK,EIF4E2,METTL21A,METTL5, MFF,MPV17,MRPL18,MTX2,NDUFB3,OST4,PDE6D, PPP1R7,PTMA,SH3BGRL3,SNRPG,SUMO1,SUMO1P3,ZBTB8OS	ARPC3,C14orf119,C8orf59,DAD1,DYNLT1,ERH,KRTCAP2, LSM2,MYL12B,PDE6D,PPP1R11,PSENEN,RAC1,RPF1, SEC61B,SF3B14,SNRPG,SRP14,TOMM6,TXN,TXNDC12

ATRAID,COA5,COPS8,CRIPT,DPY30,GPN1,MFF, MITD1,MORN2,MYEOV2,NDUFA13,ORC4,PDE6D,PSMA2, RNF181,RNF25,SNRPG,TMEM126A,TMEM126B,UBL5,USP39	ATP5O,C14orf119,C18orf21,CGRRF1,COMMD3,DCTN3,DPY30, GOLGA7,IAH1,NDUFA11,NDUFA6,NDUFV2,NSMCE2,PDE6D, PEX2,PPP1R8,SNX11,SRP14,SUPT4H1,TXNL1,UQCR11

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 PDE6D

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
DB01151	phosphodiesterase 6D, cGMP-specific, rod, delta	approved	Desipramine
DB00472	phosphodiesterase 6D, cGMP-specific, rod, delta	approved	Fluoxetine

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Cross referenced IDs for PDE6D

* 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