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 PRKCD

Basic gene info.	Gene symbol	PRKCD
	Gene name	protein kinase C, delta
	Synonyms	ALPS3\|CVID9\|MAY1\|PKCD\|nPKC-delta
	Cytomap	UCSC genome browser: 3p21.31
	Genomic location	chr3 :53195222-53226733
	Type of gene	protein-coding
	RefGenes	NM_006254.3, NM_212539.1,
	Ensembl id	ENSG00000163932
	Description	protein kinase C delta VIIIprotein kinase C delta typetyrosine-protein kinase PRKCD
	Modification date	20141222
dbXrefs	MIM : 176977
	HGNC : HGNC
	Ensembl : ENSG00000163932
	HPRD : 01501
	Vega : OTTHUMG00000133659
Protein	UniProt: Q05655 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PRKCD
	BioGPS: 5580
	Gene Expression Atlas: ENSG00000163932
	The Human Protein Atlas: ENSG00000163932
Pathway	NCI Pathway Interaction Database: PRKCD
	KEGG: PRKCD
	REACTOME: PRKCD
	ConsensusPathDB
	Pathway Commons: PRKCD
Metabolism	MetaCyc: PRKCD
	HUMANCyc: PRKCD
Regulation	Ensembl's Regulation: ENSG00000163932
	miRBase: chr3 :53,195,222-53,226,733
	TargetScan: NM_006254
	cisRED: ENSG00000163932
Context	iHOP: PRKCD
	cancer metabolism search in PubMed: PRKCD
	UCL Cancer Institute: PRKCD
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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

Cancer Description
Cancer	CGAP: PRKCD
	Familial Cancer Database: PRKCD

* 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_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM	176977; gene. 615559; phenotype.
Orphanet	1572; Common variable immunodeficiency. 300345; Autosomal recessive systemic lupus erythematosus. 3261; Autoimmune lymphoproliferative syndrome.
Disease	KEGG Disease: PRKCD
	MedGen: PRKCD (Human Medical Genetics with Condition)
	ClinVar: PRKCD
Phenotype	MGI: PRKCD (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PRKCD

Mutations for PRKCD

* 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 PRKCD 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
CA309863	PRKCD	2	487	3	53226181	53226668	TFIP11	480	648	22	26902770	26906073
BG982322	PVRL1	17	142	11	119535513	119535640	PRKCD	132	277	3	53222814	53223159
AI457515	PRKCD	3	280	3	53226458	53226733	PRKCD	275	588	3	53217182	53219666
BI021268	PRKCD	1	231	3	53219123	53219353	TBC1D8	221	490	2	101700156	101700425
AK130023	PRKCD	72	1785	3	53224514	53226919	PRKCD	1779	2041	3	53226391	53226653

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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=39)	Stat. for Synonymous SNVs (# total SNVs=18)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=1)

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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
chr3:53219628-53219628	p.S299S	3
chr3:53220653-53220653	p.D434fs*2	3
chr3:53212455-53212455	p.R6H	3
chr3:53213676-53213676	p.R67S	3
chr3:53226261-53226261	p.F670F	2
chr3:53223221-53223221	p.P568S	2
chr3:53212542-53212542	p.A35V	2
chr3:53220215-53220215	p.E373E	2
chr3:53212456-53212456	p.R6R	2
chr3:53223177-53223177	p.E553G	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	4	1		15	4		1		6			3	2				6	6		8
# mutation	4	1		13	4		1		5			3	2				7	6		10
nonsynonymous SNV	1	1		9	1		1		3			3	2				3	6		7
synonymous SNV	3			4	3				2								4			3

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
chr3:53213676	p.R67C,PRKCD	4
chr3:53217202	p.E553G,PRKCD	2
chr3:53212542	p.A213T,PRKCD	2
chr3:53226261	p.R6R,PRKCD	2
chr3:53223177	p.F670F,PRKCD	2
chr3:53219628	p.S299S,PRKCD	2
chr3:53212456	p.A35V,PRKCD	2
chr3:53212512	p.G324G,PRKCD	1
chr3:53222823	p.T526A,PRKCD	1
chr3:53215603	p.L44L,PRKCD	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 PRKCD 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 PRKCD

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.

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Protein Expression Plot (RPPA)

*RPPA protein expression data were extracted from TCPA (The Cancer Proteome Atlas). Normalized data based on replicated based normalization (RBN) was used to draw following figures.

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


APEH,ARF3,ARSG,HID1,CCDC51,CYB561D2,DALRD3, FOXA1,GPRC5A,HIST2H4A,KCTD6,NME6,NPRL2,PDHB, PRKCD,QRICH1,RNF123,SEMA3F,SPCS1,TMBIM6,TUSC2	AIFM2,AKR1C2,ANXA5,BTD,DHDDS,ELMOD3,EPHX1, FADS3,ITIH5,ITPK1,MRAP,MRAS,PHLDB1,PLXNA4, PMEPA1,PRKCD,PYGL,RETSAT,TFE3,TK2,VKORC1L1

BCAS1,C11orf86,C1orf94,CACFD1,CDHR5,CIDEC,CLDN23, DHRS9,GLRA4,IL17RE,FAM214B,LOC646627,MGLL,MYPN, PLA2G10,PRKCD,PRSS8,TMEM82,TRANK1,UGT1A4,VSIG1	APPL2,C1orf106,C2CD2L,CGN,CTSZ,DOK4,HECTD3, HHLA2,KIAA0247,LASP1,MAST2,MYO15B,PLEKHG6,PRKCD, SPINT1,TAOK3,TJP3,TRIM36,VDR,VILL,ZBTB7B

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 PRKCD

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	Q05655; -.
Chemistry	ChEMBL	CHEMBL2093867; -.
Chemistry	GuidetoPHARMACOLOGY	1485; -.
Organism-specific databases	PharmGKB	PA33763; -.
Organism-specific databases	CTD	5580; -.

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
DB04376	protein kinase C, delta	experimental	13-Acetylphorbol
DB01394	protein kinase C, delta	approved	Colchicine
DB00988	protein kinase C, delta	approved	Dopamine
DB00143	protein kinase C, delta	approved; nutraceutical	Glutathione
DB00125	protein kinase C, delta	approved; nutraceutical	L-Arginine
DB00435	protein kinase C, delta	approved	Nitric Oxide
DB00864	protein kinase C, delta	approved; investigational	Tacrolimus

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Cross referenced IDs for PRKCD

* 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