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 PNPT1

Basic gene info.	Gene symbol	PNPT1
	Gene name	polyribonucleotide nucleotidyltransferase 1
	Synonyms	COXPD13\|DFNB70\|OLD35\|PNPASE\|old-35
	Cytomap	UCSC genome browser: 2p15
	Genomic location	chr2 :55861197-55921011
	Type of gene	protein-coding
	RefGenes	NM_033109.4,
	Ensembl id	ENSG00000138035
	Description	3'-5' RNA exonuclease OLD35PNPase 1PNPase old-35polynucleotide phosphorylase 1polynucleotide phosphorylase-like proteinpolyribonucleotide nucleotidyltransferase 1, mitochondrial
	Modification date	20141207
dbXrefs	MIM : 610316
	HGNC : HGNC
	Ensembl : ENSG00000138035
	HPRD : 18493
	Vega : OTTHUMG00000129335
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PNPT1
	BioGPS: 87178
	Gene Expression Atlas: ENSG00000138035
	The Human Protein Atlas: ENSG00000138035
Pathway	NCI Pathway Interaction Database: PNPT1
	KEGG: PNPT1
	REACTOME: PNPT1
	ConsensusPathDB
	Pathway Commons: PNPT1
Metabolism	MetaCyc: PNPT1
	HUMANCyc: PNPT1
Regulation	Ensembl's Regulation: ENSG00000138035
	miRBase: chr2 :55,861,197-55,921,011
	TargetScan: NM_033109
	cisRED: ENSG00000138035
Context	iHOP: PNPT1
	cancer metabolism search in PubMed: PNPT1
	UCL Cancer Institute: PNPT1
Assigned class in ccmGDB	C

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Phenotypic Information for PNPT1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PNPT1
	Familial Cancer Database: PNPT1

* 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_PURINE_METABOLISM KEGG_PYRIMIDINE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: PNPT1
	MedGen: PNPT1 (Human Medical Genetics with Condition)
	ClinVar: PNPT1
Phenotype	MGI: PNPT1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PNPT1

Mutations for PNPT1

* 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 PNPT1 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
BI025641	PNPT1	3	310	2	55898480	55906852	PNPT1	304	390	2	55894144	55894230
BF895069	PNPT1	1	341	2	55899697	55900040	ASAP1	334	447	8	131065683	131065796
BQ378709	PNPT1	9	392	2	55882054	55894211	PNPT1	391	646	2	55873579	55883319
BQ335094	PNPT1	5	323	2	55898480	55906864	PNPT1	317	387	2	55894144	55894214

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=60)	Stat. for Synonymous SNVs (# total SNVs=12)

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
chr2:55874526-55874526	p.E520Q	3
chr2:55895069-55895069	p.Y334C	2
chr2:55863468-55863468	p.L752L	2
chr2:55863478-55863478	p.R749Q	2
chr2:55863483-55863483	p.L747L	2
chr2:55883470-55883470	p.T441A	2
chr2:55900055-55900055	p.S280L	2
chr2:55867798-55867798	p.A704A	1
chr2:55887307-55887307	p.F423F	1
chr2:55906921-55906921	p.R192Q	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	2	3		9	1		2		1	2		4	3				3	8		5
# mutation	2	3		12	1		2		1	2		4	3				3	9		6
nonsynonymous SNV	1	3		12	1		2			2		3	1				1	5		6
synonymous SNV	1								1			1	2				2	4

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
chr2:55863478	p.R749Q	2
chr2:55894127	p.Q392L	2
chr2:55872550	p.Q641Q	1
chr2:55920812	p.L367H	1
chr2:55894154	p.L117V	1
chr2:55900192	p.F620C	1
chr2:55873404	p.F340Y	1
chr2:55920850	p.S93F	1
chr2:55894164	p.N603H	1
chr2:55900197	p.Y334S	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 PNPT1 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 PNPT1

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


BUB1,CEBPZ,CENPA,DBF4,EIF2AK2,FAM136A,GTPBP4, IFIH1,MASTL,MSH2,MTIF2,NOP58,PNO1,PNPT1, PTCD3,PUS7,SUV39H2,TTK,WDR12,WDR43,XPO1	ANKRD28,C5orf22,TRAPPC13,CUL3,DHX29,DHX36,DNM1L, ESF1,FASTKD2,HSPA14,IBTK,KRR1,MFN1,NAA15, OTUD6B,PATL1,PNPT1,RRP15,SLC30A9,UBE3A,UTP15

NDUFAF7,CCDC138,CEBPZ,CPSF3,DDX18,HSPD1,HSPE1, LRPPRC,MEMO1,MRPL19,MRPL30,MTIF2,PNO1,PNPT1, PTCD3,SSB,USP39,WDR12,WDR43,WDR75,ZC3H15	ABCE1,CCDC86,DDX21,DKC1,EXOSC9,FASTKD2,GNL2, GTPBP4,MAK16,NIFK,NOP16,NOP58,ODC1,PIGW, PNPT1,RCL1,SRSF2,SRSF7,TRMT6,WDR43,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 PNPT1

There's no related Drug.

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Cross referenced IDs for PNPT1

* 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