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 PDE1C

Basic gene info.	Gene symbol	PDE1C
	Gene name	phosphodiesterase 1C, calmodulin-dependent 70kDa
	Synonyms	Hcam3\|cam-PDE 1C\|hCam-3
	Cytomap	UCSC genome browser: 7p14.3
	Genomic location	chr7 :31792631-32110980
	Type of gene	protein-coding
	RefGenes	NM_001191056.2, NM_001191057.2,NM_001191058.2,NM_001191059.2,NM_005020.3,
	Ensembl id	ENSG00000154678
	Description	Human 3',5' cyclic nucleotide phosphodiesterase (HSPDE1C1A)calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C
	Modification date	20141207
dbXrefs	MIM : 602987
	HGNC : HGNC
	Ensembl : ENSG00000154678
	HPRD : 04287
	Vega : OTTHUMG00000023836
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PDE1C
	BioGPS: 5137
	Gene Expression Atlas: ENSG00000154678
	The Human Protein Atlas: ENSG00000154678
Pathway	NCI Pathway Interaction Database: PDE1C
	KEGG: PDE1C
	REACTOME: PDE1C
	ConsensusPathDB
	Pathway Commons: PDE1C
Metabolism	MetaCyc: PDE1C
	HUMANCyc: PDE1C
Regulation	Ensembl's Regulation: ENSG00000154678
	miRBase: chr7 :31,792,631-32,110,980
	TargetScan: NM_001191056
	cisRED: ENSG00000154678
Context	iHOP: PDE1C
	cancer metabolism search in PubMed: PDE1C
	UCL Cancer Institute: PDE1C
Assigned class in ccmGDB	C

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Phenotypic Information for PDE1C(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PDE1C
	Familial Cancer Database: PDE1C

* 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: PDE1C
	MedGen: PDE1C (Human Medical Genetics with Condition)
	ClinVar: PDE1C
Phenotype	MGI: PDE1C (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PDE1C

Mutations for PDE1C

* 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
breast	PDE1C	chr7	31818064	31818064	LINS	chr15	101125974	101125974
breast	PDE1C	chr7	31965409	31965409		chr7	33676607	33676607
breast	PDE1C	chr7	31966608	31966608		chr15	90665564	90665564
breast	PDE1C	chr7	31983559	31983559		chr8	123026791	123026791
ovary	PDE1C	chr7	31963758	31963778	PDE1C	chr7	31961897	31961917
ovary	PDE1C	chr7	32046598	32046618	PDE1C	chr7	32046664	32046684

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 PDE1C 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
H11830	SETX	1	348	9	135145001	135150759	PDE1C	336	358	7	32108935	32108957
AV724221	PDE1C	1	425	7	32088724	32089152	LAT2	421	604	7	73643778	73643964
AA247844	PDE1C	1	201	7	31825611	31825812	PDE1C	196	255	7	31829557	31829617

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	ns	ovary	pancre	prost	skin	stoma	thyro	urina
Total # sample	2	2				1	3		7		1		1		1	1	5
GAIN (# sample)	1	2				1	3		6		1		1		1	1	5
LOSS (# sample)	1								1

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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=133)	Stat. for Synonymous SNVs (# total SNVs=34)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=1)
There's no deleted 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
chr7:31904603-31904603	p.D235N	4
chr7:31890295-31890295	p.E271Q	4
chr7:32109912-32109912	p.R32C	4
chr7:31918727-31918727	p.R103*	4
chr7:31864483-31864483	p.S468S	3
chr7:31862716-31862716	p.R518Q	3
chr7:31855568-31855568	p.E595K	3
chr7:31890286-31890286	p.G274R	3
chr7:31864484-31864484	p.S468L	3
chr7:31917638-31917638	p.R146Q	3

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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=5

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	4	3	1	17	4		9		1	1		26	13	4	1	2	47	11		14
# mutation	4	3	1	17	4		9		1	1		30	15	4	1	2	63	11		16
nonsynonymous SNV	3	2	1	14	4		7		1			18	12	4		1	42	5		10
synonymous SNV	1	1		3			2			1		12	3		1	1	21	6		6

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
chr7:31855568	p.P493P,PDE1C	3
chr7:31864484	p.E595K,PDE1C	3
chr7:31862790	p.S468W,PDE1C	3
chr7:31855724	p.T254M,PDE1C	2
chr7:31890345	p.R46Q	2
chr7:31862779	p.S497Y,PDE1C	2
chr7:32109934	p.D235N,PDE1C	2
chr7:31904603	p.R146Q,PDE1C	2
chr7:31855612	p.A543T,PDE1C	2
chr7:32209516	p.A361V,PDE1C	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 PDE1C 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 PDE1C

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


A2M,ANKRD1,CHST3,CYP1A2,FAM126A,GRAMD3,GRIN2A, HEPH,ISM1,KLHL38,LOC285830,MAML2,OR2S2,PALM2, PALM2-AKAP2,PDE1C,PROS1,SLC7A5P1,SOCS5,TTC7A,WWTR1	ABI2,ARHGAP19,CACNA1C,ESYT3,FAM83B,FAT2,GPR75, GTF3C4,ITGA2,KIAA1217,LY75,NFASC,PAK3,PAK7, PAWR,PCNXL2,PDE1C,SEMA5A,SIPA1L1,ZNF37BP,ZNF618

ABCG4,ADAMTS3,AKT3,CD93,CYP46A1,DYSF,EHD3, GIPC3,IL7R,KIAA1614,LPHN2,NHSL2,PDE1C,PREX2, PTPRN,RPH3A,SCN1B,SDK1,SLC6A17,XKR5,ZNF366	ABCA8,BMPER,PCNXL4,DIEXF,TRMT44,ERCC6L2,EIF2AK4, FMNL2,IRAK3,KIAA0355,LOX,MYH13,PDE1C,PREX2, PRLHR,RCAN2,SDK2,SHPRH,TGFBRAP1,TTC37,TXLNG

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 PDE1C

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 1C, calmodulin-dependent 70kDa	approved	Desipramine

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Cross referenced IDs for PDE1C

* 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