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 PDE6C

Basic gene info.	Gene symbol	PDE6C
	Gene name	phosphodiesterase 6C, cGMP-specific, cone, alpha prime
	Synonyms	ACHM5\|COD4\|PDEA2
	Cytomap	UCSC genome browser: 10q24
	Genomic location	chr10 :95372344-95425429
	Type of gene	protein-coding
	RefGenes	NM_006204.3,
	Ensembl id	ENSG00000095464
	Description	cGMP phosphodiesterase 6Ccone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'
	Modification date	20141219
dbXrefs	MIM : 600827
	HGNC : HGNC
	Ensembl : ENSG00000095464
	HPRD : 02898
	Vega : OTTHUMG00000018775
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PDE6C
	BioGPS: 5146
	Gene Expression Atlas: ENSG00000095464
	The Human Protein Atlas: ENSG00000095464
Pathway	NCI Pathway Interaction Database: PDE6C
	KEGG: PDE6C
	REACTOME: PDE6C
	ConsensusPathDB
	Pathway Commons: PDE6C
Metabolism	MetaCyc: PDE6C
	HUMANCyc: PDE6C
Regulation	Ensembl's Regulation: ENSG00000095464
	miRBase: chr10 :95,372,344-95,425,429
	TargetScan: NM_006204
	cisRED: ENSG00000095464
Context	iHOP: PDE6C
	cancer metabolism search in PubMed: PDE6C
	UCL Cancer Institute: PDE6C
Assigned class in ccmGDB	C

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Phenotypic Information for PDE6C(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PDE6C
	Familial Cancer Database: PDE6C

* 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: PDE6C
	MedGen: PDE6C (Human Medical Genetics with Condition)
	ClinVar: PDE6C
Phenotype	MGI: PDE6C (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PDE6C

Mutations for PDE6C

* 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

* 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
ovary	PDE6C	chr10	95411408	95411428	FRA10AC1	chr10	95434104	95434124

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 PDE6C 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

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=74)	Stat. for Synonymous SNVs (# total SNVs=22)

Stat. for Deletions (# total SNVs=7)	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
chr10:95422929-95422929	p.E838K	4
chr10:95385332-95385332	p.E289K	3
chr10:95399866-95399866	p.E508K	2
chr10:95372905-95372905	p.G141G	2
chr10:95394661-95394661	p.T422T	2
chr10:95405773-95405773	p.L635Q	2
chr10:95400236-95400236	p.R553R	2
chr10:95395245-95395245	p.?	2
chr10:95372764-95372764	p.D94D	2
chr10:95395293-95395293	p.D437N	2

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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=3

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	6		11			4		3	1		8	3	3		1	27	8		10
# mutation	3	6		10			4		3	1		9	3	3		1	31	9		12
nonsynonymous SNV	2	6		7			2		3			6	1	2		1	20	3		10
synonymous SNV	1			3			2			1		3	2	1			11	6		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
chr10:95399952	p.E838K	2
chr10:95372619	p.R553R	2
chr10:95385332	p.T422T	2
chr10:95395327	p.A8A	2
chr10:95422929	p.R448I	2
chr10:95399866	p.E508K	2
chr10:95400236	p.L179L	2
chr10:95400746	p.S46Y	2
chr10:95380445	p.E289K	2
chr10:95372506	p.D603N	2

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 PDE6C 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 PDE6C

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


C3orf22,FAM71B,GLT6D1,HIST1H2BA,IL17F,KRTAP10-12,LOC390858, LOC643719,LOC732275,OR1K1,OR4X1,OR5AS1,OR8B3,OR8K1, OR9I1,OR9Q2,PDE6C,PNLIP,SYCP3,TRIM63,VPREB1	BTBD18,TMEM51-AS1,KIAA1456,N4BP2L2-IT2,ENC1,FRMD5,HOXA2, LOC92973,NAP1L2,PDE6C,PKNOX1,RIMS3,SPACA4,TDRD6, TMPRSS11B,UNC119B,USP31,ZNF19,ZNF230,ZNF470,ZNF540

MRGPRG-AS1,C12orf50,LAMP5,C3orf35,CARNS1,DGKB,FGF3, LOC100131551,LOC144776,LRRC36,MAEL,MSTN,NTF4,PDE6C, OOSP2,SACS,SCN2A,SERPINB12,SPANXN2,TM9SF1,UPP2	AKAP8,EGFEM1P,DNAH17,EDNRB,F3,GNRH1,KRT38, LOC100240726,LOC220729,LRIG2,LY6G5B,NCRNA00120,PDE6C,PRKY, LTN1,SNORA8,SYCP2,TAS2R4,TBC1D3P2,TTTY2,ZBTB18

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 PDE6C

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 6C, cGMP-specific, cone, alpha prime	approved	Desipramine
DB00472	phosphodiesterase 6C, cGMP-specific, cone, alpha prime	approved	Fluoxetine

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Cross referenced IDs for PDE6C

* 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