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 PLCD4

Basic gene info.	Gene symbol	PLCD4
	Gene name	phospholipase C, delta 4
	Synonyms	-
	Cytomap	UCSC genome browser: 2q35
	Genomic location	chr2 :219472487-219501909
	Type of gene	protein-coding
	RefGenes	NM_032726.3,
	Ensembl id	ENSG00000115556
	Description	1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-41-phosphatidylinositol-4,5-bisphosphate phosphodiesterase delta-4PLC delta4phosphoinositide phospholipase C-delta-4
	Modification date	20141207
dbXrefs	MIM : 605939
	HGNC : HGNC
	Ensembl : ENSG00000115556
	HPRD : 07296
	Vega : OTTHUMG00000154743
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PLCD4
	BioGPS: 84812
	Gene Expression Atlas: ENSG00000115556
	The Human Protein Atlas: ENSG00000115556
Pathway	NCI Pathway Interaction Database: PLCD4
	KEGG: PLCD4
	REACTOME: PLCD4
	ConsensusPathDB
	Pathway Commons: PLCD4
Metabolism	MetaCyc: PLCD4
	HUMANCyc: PLCD4
Regulation	Ensembl's Regulation: ENSG00000115556
	miRBase: chr2 :219,472,487-219,501,909
	TargetScan: NM_032726
	cisRED: ENSG00000115556
Context	iHOP: PLCD4
	cancer metabolism search in PubMed: PLCD4
	UCL Cancer Institute: PLCD4
Assigned class in ccmGDB	C

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Phenotypic Information for PLCD4(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PLCD4
	Familial Cancer Database: PLCD4

* 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_INOSITOL_PHOSPHATE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: PLCD4
	MedGen: PLCD4 (Human Medical Genetics with Condition)
	ClinVar: PLCD4
Phenotype	MGI: PLCD4 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PLCD4

Mutations for PLCD4

* 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

There's no inter-chromosomal structural variation.

- 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	PLCD4	chr2	219492269	219492289		chr2	218124122	218124142

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 PLCD4 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
BQ183357	ARF1	19	512	1	228286417	228286910	PLCD4	510	690	2	219500615	219501106
BX102201	PLCD4	1	410	2	219488760	219489169	MARC2	407	512	1	220932026	220932131
CV404934	XXYLT1	10	148	3	194878771	194878912	PLCD4	145	217	2	219498978	219499050

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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=45)	Stat. for Synonymous SNVs (# total SNVs=13)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	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
chr2:219487409-219487409	p.E194*	3
chr2:219499340-219499340	p.T628N	2
chr2:219480467-219480467	p.A2V	2
chr2:219486299-219486299	p.E173*	2
chr2:219499248-219499248	p.G597G	1
chr2:219492801-219492801	p.C274*	1
chr2:219501002-219501002	p.R690Q	1
chr2:219483332-219483332	p.N71T	1
chr2:219494318-219494318	p.G351R	1
chr2:219498359-219498359	p.S494F	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	2		4			2		3			6	3	3		1	5	2	1	8
# mutation	3	2		4			2		3			6	3	3		1	7	2	1	10
nonsynonymous SNV	2	1		3			2		2			4		3		1	3	1	1	8
synonymous SNV	1	1		1					1			2	3				4	1		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
chr2:219498867	p.R549H	2
chr2:219498429	p.Q637K	1
chr2:219483489	p.L125I	1
chr2:219499329	p.K435E	1
chr2:219492945	p.A667V	1
chr2:219498439	p.E169K	1
chr2:219483493	p.E458Q	1
chr2:219500531	p.T686K	1
chr2:219494296	p.E194K	1
chr2:219498441	p.E462K	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 PLCD4 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 PLCD4

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


ABCA2,AFF3,ASB16,C8orf86,CACNA2D2,COQ10A,DNAJC12, DNALI1,FAM57B,GATA3,ICA1L,INPP5J,KCTD6,CCDC183, LYPD6B,MAP3K12,NEURL1,P4HTM,PLCD4,RELL1,SEMA3F	RBFOX1,ASB16,MLIP,CA3,CACNG1,CALML6,CKMT2, CLCN1,CMYA5,CTNNA3,FBXO40,MYH1,MYH7B,MYOZ3, PGAM2,PKIA,PLCD4,PYGM,SLC25A4,SLC36A2,TMEM38A

APOBEC2,ASTN1,ATCAY,ATP2B3,DKFZP434L187,DPYSL5,GPR26, GRIN2A,IGSF11,JPH4,LOC200726,NRXN1,PCSK2,PLCD4, RPRM,SCN1A,SLC7A14,SYT6,THSD7B,TMEM59L,UNC80	ASIC1,ATP1A2,ATP2B4,BVES,CA14,CACNA1H,DACT3, KCNH2,KY,LDB3,MPP2,NPTXR,NRXN2,PLCD4, PTGS1,PYGM,SLC8A2,SMTN,SPEG,TACR2,TGFB1I1

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 PLCD4

There's no related Drug.

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Cross referenced IDs for PLCD4

* 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