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 PRMT5

Basic gene info.	Gene symbol	PRMT5
	Gene name	protein arginine methyltransferase 5
	Synonyms	HRMT1L5\|IBP72\|JBP1\|SKB1\|SKB1Hs
	Cytomap	UCSC genome browser: 14q11.2
	Genomic location	chr14 :23389732-23398661
	Type of gene	protein-coding
	RefGenes	NM_001039619.2, NM_001282953.1,NM_001282954.1,NM_001282955.1,NM_001282956.1, NM_006109.4,
	Ensembl id	ENSG00000100462
	Description	72 kDa ICln-binding proteinHMT1 hnRNP methyltransferase-like 5SKB1 homologhistone-arginine N-methyltransferase PRMT5jak-binding protein 1protein arginine N-methyltransferase 5shk1 kinase-binding protein 1 homolog
	Modification date	20141222
dbXrefs	MIM : 604045
	HGNC : HGNC
	Ensembl : ENSG00000100462
	HPRD : 04955
	Vega : OTTHUMG00000028709
Protein	UniProt: O14744 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PRMT5
	BioGPS: 10419
	Gene Expression Atlas: ENSG00000100462
	The Human Protein Atlas: ENSG00000100462
Pathway	NCI Pathway Interaction Database: PRMT5
	KEGG: PRMT5
	REACTOME: PRMT5
	ConsensusPathDB
	Pathway Commons: PRMT5
Metabolism	MetaCyc: PRMT5
	HUMANCyc: PRMT5
Regulation	Ensembl's Regulation: ENSG00000100462
	miRBase: chr14 :23,389,732-23,398,661
	TargetScan: NM_001039619
	cisRED: ENSG00000100462
Context	iHOP: PRMT5
	cancer metabolism search in PubMed: PRMT5
	UCL Cancer Institute: PRMT5
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PRMT5 in cancer cell metabolism	1. Kanamaluru D, Xiao Z, Fang S, Choi S-E, Kim D-H, et al. (2011) Arginine methylation by PRMT5 at a naturally occurring mutation site is critical for liver metabolic regulation by small heterodimer partner. Molecular and cellular biology 31: 1540-1550. go to article

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Phenotypic Information for PRMT5(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PRMT5
	Familial Cancer Database: PRMT5

* 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_NON_CODING_RNA REACTOME_METABOLISM_OF_RNA

Others
OMIM	604045; gene. 604045; gene.
Orphanet
Disease	KEGG Disease: PRMT5
	MedGen: PRMT5 (Human Medical Genetics with Condition)
	ClinVar: PRMT5
Phenotype	MGI: PRMT5 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PRMT5

Mutations for PRMT5

* 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 PRMT5 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
CD696469	MYL12A	19	136	18	3247829	3253269	PRMT5	133	624	14	23393859	23395990
BE063150	PRMT5	2	83	14	23391404	23391687	PRMT5	77	289	14	23394138	23395442
BE063240	PRMT5	115	215	14	23395342	23395442	PRMT5	205	469	14	23390106	23391691
DA812278	PRMT5	1	392	14	23391665	23398585	DLG2	393	415	11	85013461	85013483

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=38)	Stat. for Synonymous SNVs (# total SNVs=8)

Stat. for Deletions (# total SNVs=1)	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
chr14:23393903-23393903	p.L319V	3
chr14:23393722-23393722	p.R348*	2
chr14:23398551-23398551	p.G7V	2
chr14:23391451-23391451	p.?	2
chr14:23393852-23393852	p.Q336E	2
chr14:23397790-23397790	p.R49C	2
chr14:23397792-23397792	p.P48L	2
chr14:23397352-23397352	p.R100C	2
chr14:23395506-23395506	p.?	2
chr14:23397411-23397411	p.T80M	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	4	1	7			2		3			6	1	3		2	5	2		8
# mutation	3	4	1	8			2		3			6	1	3		2	6	2		9
nonsynonymous SNV	3	3		6			2		3			5	1	3		1	5	2		7
synonymous SNV		1	1	2								1				1	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
chr14:23397352	p.R83C,PRMT5	2
chr14:23397792	p.P31Q,PRMT5	2
chr14:23394198	p.K438K,PRMT5	1
chr14:23390200	p.I161M,PRMT5	1
chr14:23396819	p.F61L,PRMT5	1
chr14:23393546	p.R422L,PRMT5	1
chr14:23398392	p.P140Q,PRMT5	1
chr14:23394235	p.S86S,PRMT5	1
chr14:23390249	p.R363C,PRMT5	1
chr14:23397341	p.L128L,PRMT5	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 PRMT5 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 PRMT5

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


APEX1,C14orf119,NOP9,DAD1,DCAF11,HAUS4,HOMEZ, IPO4,NGDN,OXA1L,PARP2,PRMT5,PSMB5,RBM23, RNF31,SCAF11___GEMIN2___ZEB2,SUPT16H,THTPA,TINF2,TM9SF1,TOX4	C10orf2,DKC1,EEF1G,FBL,GLB1L2,GSTO2,HSP90AB1, IMPDH2,IPO4,KDM1A,DANCR,NONO,PGAP2,POLR1C, PRMT5,RAB25,RPL10A,RPS18,TMC4,TMEM177,UBIAD1

APEX1,CDCA4,CDKN3,DLGAP5,DLST,EIF2B2,EIF2S1, FNTB,GNPNAT1,MTHFD1,PARP2,PNP,PRMT5,PSMB5, SCAF11___GEMIN2___ZEB2,SNW1,SUPT16H,TMX1,TRMT5,VRK1,WDHD1	APEX1,CCT2,CDCA4,EBNA1BP2,EXOSC2,FARSB,GNL3, MRPL3,NHP2L1,NOP56,NPM3,NUP35,NUP37,POLR1C, PRMT1,PRMT5,SRP72,SUV39H2,TFDP1,UTP6,WDR77

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 PRMT5

There's no related Drug.

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Cross referenced IDs for PRMT5

* 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