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 PRKCSH

Basic gene info.	Gene symbol	PRKCSH
	Gene name	protein kinase C substrate 80K-H
	Synonyms	AGE-R2\|G19P1\|PCLD\|PKCSH\|PLD1
	Cytomap	UCSC genome browser: 19p13.2
	Genomic location	chr19 :11546268-11561782
	Type of gene	protein-coding
	RefGenes	NM_001001329.2, NM_001289102.1,NM_001289103.1,NM_001289104.1,NM_002743.3,
	Ensembl id	ENSG00000130175
	Description	AGE-binding receptor 2glucosidase 2 subunit betaglucosidase II subunit betahepatocystinprotein kinase C substrate 60.1 kDa protein heavy chainprotein kinase C substrate, 80 Kda protein
	Modification date	20141207
dbXrefs	MIM : 177060
	HGNC : HGNC
	Ensembl : ENSG00000130175
	HPRD : 03518
	Vega : OTTHUMG00000182029
Protein	UniProt: P14314 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PRKCSH
	BioGPS: 5589
	Gene Expression Atlas: ENSG00000130175
	The Human Protein Atlas: ENSG00000130175
Pathway	NCI Pathway Interaction Database: PRKCSH
	KEGG: PRKCSH
	REACTOME: PRKCSH
	ConsensusPathDB
	Pathway Commons: PRKCSH
Metabolism	MetaCyc: PRKCSH
	HUMANCyc: PRKCSH
Regulation	Ensembl's Regulation: ENSG00000130175
	miRBase: chr19 :11,546,268-11,561,782
	TargetScan: NM_001001329
	cisRED: ENSG00000130175
Context	iHOP: PRKCSH
	cancer metabolism search in PubMed: PRKCSH
	UCL Cancer Institute: PRKCSH
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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

Cancer Description
Cancer	CGAP: PRKCSH
	Familial Cancer Database: PRKCSH

* 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
REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM	174050; phenotype. 177060; gene.
Orphanet	2924; Isolated polycystic liver disease.
Disease	KEGG Disease: PRKCSH
	MedGen: PRKCSH (Human Medical Genetics with Condition)
	ClinVar: PRKCSH
Phenotype	MGI: PRKCSH (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PRKCSH

Mutations for PRKCSH

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PRKCSH 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
BE938446	PRKCSH	4	144	19	11556241	11557903	PRKCSH	132	264	19	11557937	11558347
BF746637	PRKCSH	38	112	19	11560087	11560161	PRKCSH	106	313	19	11556248	11557976
AI467862	PRKCSH	10	150	19	11561643	11561783	ENC1	146	494	5	73931210	73931558
CN412416	NDUFA7	1	213	19	8381403	8386227	PRKCSH	210	566	19	11556248	11558406
AA282178	PRKCSH	6	135	19	11561654	11561783	PURB	131	332	7	44919088	44919289
DB266941	LOC100507412	1	151	?	112029	112179	PRKCSH	152	585	19	11546452	11548781
BI001011	NFE2L1	23	159	17	46133392	46133531	PRKCSH	156	469	19	11553215	11557922
AA968638	DYSF	1	186	2	71913708	71913893	PRKCSH	178	444	19	11556212	11558280
AU120749	PRKCSH	1	512	19	11558391	11560138	PRKCSH	511	615	19	11547220	11547325
BF742989	PRKCSH	30	107	19	11556212	11556289	MEF2A	93	308	15	100250918	100252761
BE773523	PRKCSH	1	62	19	11557098	11557160	GANAB	55	159	11	62407307	62407411

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=4

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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=5)	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
chr19:11558370-11558370	p.E322E	4
chr19:11558341-11558343	p.E313delE	3
chr19:11558265-11558265	p.T287T	2
chr19:11556233-11556233	p.E210K	2
chr19:11548778-11548778	p.N93S	2
chr19:11559362-11559362	p.E395K	2
chr19:11559794-11559794	p.T444I	2
chr19:11559895-11559895	p.W449R	1
chr19:11547013-11547013	p.L25L	1
chr19:11558261-11558261	p.P286L	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	1	1	1	5	2				1			3	4	1		3	2	4		5
# mutation	1	1	1	5	2				1			3	4	1		3	2	4		8
nonsynonymous SNV	1	1		3	2				1			1	1			2	1	3		7
synonymous SNV			1	2								2	3	1		1	1	1		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
chr19:11558373	p.E323E,PRKCSH	2
chr19:11547013	p.L25L,PRKCSH	1
chr19:11560204	p.P347P,PRKCSH	1
chr19:11558265	p.E519K,PRKCSH	1
chr19:11559742	p.L40V,PRKCSH	1
chr19:11547248	p.E375K,PRKCSH	1
chr19:11558317	p.C56C,PRKCSH	1
chr19:11559765	p.E394D,PRKCSH	1
chr19:11547298	p.G73D,PRKCSH	1
chr19:11558330	p.Y413Y,PRKCSH	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 PRKCSH 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 PRKCSH

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


C19orf43,C19orf52,CCDC124,CDC37,COPE,ECSIT,EIF3G, ELOF1,FARSA,FKBP8,MRPL4,PIN1,PPAN,PRKCSH, QTRT1,RAD23A,STX10,TMED1,TMEM161A,YIPF2,ZNF653	C9orf114,DDX49,DDX54,EHMT2,FARSA,GTF2F1,HMG20B, LRRC45,MAN1B1,PES1,PRKCSH,RBM10,RPUSD1,RRP1, RUVBL2,TCF25,TRIM28,TSC22D4,NELFA,XAB2,XRCC1

AKAP8L,BAG6,EIF3G,FKBP8,FOXA2,FOXP4,GLTSCR2, LRP5,MED25,PRKCSH,RAB11B,RNF44,SAFB2,SAFB, SART1,SF3A2,SUGP1,SMARCA4,UBXN1,UPF1,XAB2	ABHD15,AGPAT3,ATG9A,BAG6,CLPTM1,EPN1,GIT1, INSR,KIAA0195,LRP5,MAP3K11,OS9,P4HA2,POMT1, PRKCSH,PTPRF,RFX1,SORL1,ZNF592,ZNF687,ZNF768

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 PRKCSH

There's no related Drug.

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Cross referenced IDs for PRKCSH

* 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