Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolPARN
Gene namepoly(A)-specific ribonuclease
SynonymsDAN
CytomapUCSC genome browser: 16p13
Genomic locationchr16 :14529556-14724128
Type of geneprotein-coding
RefGenesNM_001134477.2,
NM_001242992.1,NM_002582.3,
Ensembl idENSG00000140694
Descriptiondeadenylating nucleasedeadenylation nucleasepoly(A)-specific ribonuclease (deadenylation nuclease)poly(A)-specific ribonuclease PARNpolyadenylate-specific ribonuclease
Modification date20141207
dbXrefs MIM : 604212
HGNC : HGNC
Ensembl : ENSG00000140694
HPRD : 07250
Vega : OTTHUMG00000173199
ProteinUniProt: O95453
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PARN
BioGPS: 5073
Gene Expression Atlas: ENSG00000140694
The Human Protein Atlas: ENSG00000140694
PathwayNCI Pathway Interaction Database: PARN
KEGG: PARN
REACTOME: PARN
ConsensusPathDB
Pathway Commons: PARN
MetabolismMetaCyc: PARN
HUMANCyc: PARN
RegulationEnsembl's Regulation: ENSG00000140694
miRBase: chr16 :14,529,556-14,724,128
TargetScan: NM_001134477
cisRED: ENSG00000140694
ContextiHOP: PARN
cancer metabolism search in PubMed: PARN
UCL Cancer Institute: PARN
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PARN in cancer cell metabolism1. 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)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_MRNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM 604212; gene.
Orphanet
DiseaseKEGG Disease: PARN
MedGen: PARN (Human Medical Genetics with Condition)
ClinVar: PARN
PhenotypeMGI: PARN (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
breastPARNchr161455380114553801GGA2chr162351308323513083
pancreasPARNchr161469983314699853PARNchr161470803814708058
pancreasPARNchr161470758114707601XPO6chr162820310028203120
pancreasPARNchr161471560014715620PARNchr161469779214697812
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PARN related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW857210PARN105354161470527014705648GOLPH334955453212621532126420
DA139780ZNF5872209195828103958281246PARN208580161454075814576686
AI207461CFB1113632518813252074PARN100671161456530814565880
AW889901PARN40231161468742014687611PARN227500161468013514687347
BG572766PARN7382161470461314723490MALAT1372740116527014865270515
AF130116CFB1113632518813252074PARN1002438161456354414565880
AW889893PARN1192161468742014687611PARN188450161468013514687336

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample          1   1  
GAIN (# sample)          1      
LOSS (# sample)              1  
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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr16:14576651-14576651p.R505Q3
chr16:14698008-14698008p.E260*2
chr16:14687203-14687203p.L291L1
chr16:14540788-14540788p.K607N1
chr16:14704540-14704540p.T172M1
chr16:14645891-14645891p.E489E1
chr16:14720998-14720998p.N98D1
chr16:14687209-14687209p.M289I1
chr16:14540793-14540793p.K606E1
chr16:14704541-14704541p.T172A1

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample  381   1  722  54 8
# mutation  381   1  722  55 9
nonsynonymous SNV  341   1  412  55 6
synonymous SNV   5       31      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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr16:14576651p.R459Q,PARN3
chr16:14576608p.E473E,PARN2
chr16:14693769p.K560E,PARN1
chr16:14530620p.Y335Y,PARN1
chr16:14711498p.T24T,PARN1
chr16:14693794p.S556L,PARN1
chr16:14540788p.S263R,PARN1
chr16:14720998p.K14R,PARN1
chr16:14576652p.E544Q,PARN1
chr16:14693805p.V247A,PARN1

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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



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