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 PARN

Basic gene info.	Gene symbol	PARN
	Gene name	poly(A)-specific ribonuclease
	Synonyms	DAN
	Cytomap	UCSC genome browser: 16p13
	Genomic location	chr16 :14529556-14724128
	Type of gene	protein-coding
	RefGenes	NM_001134477.2, NM_001242992.1,NM_002582.3,
	Ensembl id	ENSG00000140694
	Description	deadenylating nucleasedeadenylation nucleasepoly(A)-specific ribonuclease (deadenylation nuclease)poly(A)-specific ribonuclease PARNpolyadenylate-specific ribonuclease
	Modification date	20141207
dbXrefs	MIM : 604212
	HGNC : HGNC
	Ensembl : ENSG00000140694
	HPRD : 07250
	Vega : OTTHUMG00000173199
Protein	UniProt: O95453 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PARN
	BioGPS: 5073
	Gene Expression Atlas: ENSG00000140694
	The Human Protein Atlas: ENSG00000140694
Pathway	NCI Pathway Interaction Database: PARN
	KEGG: PARN
	REACTOME: PARN
	ConsensusPathDB
	Pathway Commons: PARN
Metabolism	MetaCyc: PARN
	HUMANCyc: PARN
Regulation	Ensembl's Regulation: ENSG00000140694
	miRBase: chr16 :14,529,556-14,724,128
	TargetScan: NM_001134477
	cisRED: ENSG00000140694
Context	iHOP: PARN
	cancer metabolism search in PubMed: PARN
	UCL Cancer Institute: PARN
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PARN in cancer cell metabolism	1. AA Balatsos N, Maragozidis P, Anastasakis D, Stathopoulos C (2012) Modulation of poly (A)-specific ribonuclease (PARN): current knowledge and perspectives. Current medicinal chemistry 19: 4838-4849. go to article

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

Cancer Description
Cancer	CGAP: PARN
	Familial Cancer Database: PARN

* 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_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM	604212; gene.
Orphanet
Disease	KEGG Disease: PARN
	MedGen: PARN (Human Medical Genetics with Condition)
	ClinVar: PARN
Phenotype	MGI: PARN (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PARN

Mutations for PARN

* 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

There's no intra-chromosomal structural variation.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
breast	PARN	chr16	14553801	14553801	GGA2	chr16	23513083	23513083
pancreas	PARN	chr16	14699833	14699853	PARN	chr16	14708038	14708058
pancreas	PARN	chr16	14707581	14707601	XPO6	chr16	28203100	28203120
pancreas	PARN	chr16	14715600	14715620	PARN	chr16	14697792	14697812

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 PARN 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
AW857210	PARN	105	354	16	14705270	14705648	GOLPH3	349	554	5	32126215	32126420
DA139780	ZNF587	2	209	19	58281039	58281246	PARN	208	580	16	14540758	14576686
AI207461	CFB	1	113	6	3251881	3252074	PARN	100	671	16	14565308	14565880
AW889901	PARN	40	231	16	14687420	14687611	PARN	227	500	16	14680135	14687347
BG572766	PARN	7	382	16	14704613	14723490	MALAT1	372	740	11	65270148	65270515
AF130116	CFB	1	113	6	3251881	3252074	PARN	100	2438	16	14563544	14565880
AW889893	PARN	1	192	16	14687420	14687611	PARN	188	450	16	14680135	14687336

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=30)	Stat. for Synonymous SNVs (# total SNVs=11)

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
chr16:14576651-14576651	p.R505Q	3
chr16:14698008-14698008	p.E260*	2
chr16:14530583-14530583	p.D637D	1
chr16:14702917-14702917	p.T206T	1
chr16:14576629-14576629	p.Y512Y	1
chr16:14711476-14711476	p.G120E	1
chr16:14687159-14687159	p.A306V	1
chr16:14530615-14530615	p.N627Y	1
chr16:14702941-14702941	p.K198N	1
chr16:14711480-14711480	p.Q119*	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	8	1				1			7	2	2			5	4		8
# mutation			3	8	1				1			7	2	2			5	5		9
nonsynonymous SNV			3	4	1				1			4	1	2			5	5		6
synonymous SNV				5								3	1							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
chr16:14576651	p.R459Q,PARN	3
chr16:14576608	p.E473E,PARN	2
chr16:14530583	p.N581Y,PARN	1
chr16:14711452	p.S438Y,PARN	1
chr16:14576590	p.F75C,PARN	1
chr16:14680212	p.S579S,PARN	1
chr16:14530615	p.M382I,PARN	1
chr16:14711473	p.G74E,PARN	1
chr16:14687198	p.I67V,PARN	1
chr16:14530619	p.S579L,PARN	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 PARN 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 PARN

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


BFAR,C16orf62,FOPNL,C16orf72,KNOP1,CLUAP1,COG7, COQ7,EARS2,ERI2,GSPT1,HN1L,IQCK,LYRM1, PARN,RNF40,RRN3,THUMPD1,USP7,ZNF174,ZSCAN32	AP1M2,APTX,ARFIP2,C1orf210,COG7,CSTF3,DLG3, EIF2AK1,EPCAM,EXOSC10,SPIDR,NIPSNAP1,NVL,PARN, SEC23B,SUSD4,NELFCD,THADA,UMPS,XRCC5,ZNF544

BRD7,ENKD1,USB1,CCDC101,CDIPT,CDR2,CFDP1, COG7,DEXI,FAM192A,EEF2KMT,IST1,NSMCE1,PARN, RNF40,RNPS1,STX4,TFAP4,USP7,VAC14,ZNF19	CNOT4,DYNLL2,DYRK1A,EIF4H,GRB2,HNRNPUL1,HNRNPUL2, HTATSF1,KIDINS220,KAT6A,PAF1,PARN,RAB3GAP1,RSF1, SNRNP200,SUPT6H,TAF15,THRAP3,UPF2,WDR7,ZNF407

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 PARN

There's no related Drug.

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Cross referenced IDs for PARN

* 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