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 TPR

Basic gene info.	Gene symbol	TPR
	Gene name	translocated promoter region, nuclear basket protein
	Synonyms	-
	Cytomap	UCSC genome browser: 1q25
	Genomic location	chr1 :186280785-186344457
	Type of gene	protein-coding
	RefGenes	NM_003292.2,
	Ensembl id	ENSG00000047410
	Description	NPC-associated intranuclear proteinmegatornuclear pore complex-associated protein TPRnucleoprotein TPRtranslocated promoter region (to activated MET oncogene)translocated promoter region proteintumor potentiating region
	Modification date	20141221
dbXrefs	MIM : 189940
	HGNC : HGNC
	Ensembl : ENSG00000047410
	HPRD : 08927
	Vega : OTTHUMG00000035580
Protein	UniProt: P12270 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TPR
	BioGPS: 7175
	Gene Expression Atlas: ENSG00000047410
	The Human Protein Atlas: ENSG00000047410
Pathway	NCI Pathway Interaction Database: TPR
	KEGG: TPR
	REACTOME: TPR
	ConsensusPathDB
	Pathway Commons: TPR
Metabolism	MetaCyc: TPR
	HUMANCyc: TPR
Regulation	Ensembl's Regulation: ENSG00000047410
	miRBase: chr1 :186,280,785-186,344,457
	TargetScan: NM_003292
	cisRED: ENSG00000047410
Context	iHOP: TPR
	cancer metabolism search in PubMed: TPR
	UCL Cancer Institute: TPR
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of TPR in cancer cell metabolism	1. Tankiewicz A, Dziemiańczyk D, Buczko P, Szarmach I, Grabowska S, et al. (2005) Tryptophan and its metabolites in patients with oral squamous cell carcinoma: preliminary study. Advances in medical sciences 51: 221-224. go to article

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

Cancer Description
Cancer	CGAP: TPR
	Familial Cancer Database: TPR

* 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 REACTOME_METABOLISM_OF_CARBOHYDRATES

Others
OMIM	188550; phenotype. 189940; gene.
Orphanet	146; Papillary or follicular thyroid carcinoma.
Disease	KEGG Disease: TPR
	MedGen: TPR (Human Medical Genetics with Condition)
	ClinVar: TPR
Phenotype	MGI: TPR (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: TPR

Mutations for TPR

* 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 TPR related fusion information.

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

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=6

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=189)	Stat. for Synonymous SNVs (# total SNVs=47)

Stat. for Deletions (# total SNVs=4)	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
chr1:186289548-186289548	p.S2155L	5
chr1:186319501-186319501	p.K877R	3
chr1:186302435-186302435	p.S1758S	3
chr1:186321204-186321204	p.L791L	2
chr1:186319500-186319500	p.K877N	2
chr1:186315342-186315342	p.K1007N	2
chr1:186319502-186319502	p.K877E	2
chr1:186321231-186321231	p.E782D	2
chr1:186340095-186340095	p.?	2
chr1:186321242-186321242	p.V779I	2

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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=5

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	11	11	2	34	3		5	1	10			18	19	2		2	18	19		26
# mutation	12	12	2	30	3		5	1	10			21	21	2		2	19	26		38
nonsynonymous SNV	10	11	1	21	2		5	1	6			16	17			2	12	21		32
synonymous SNV	2	1	1	9	1				4			5	4	2			7	5		6

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
chr1:186289548	p.S2155L	5
chr1:186302435	p.S1758S	3
chr1:186319501	p.K877N	2
chr1:186296594	p.K877R	2
chr1:186303547	p.R1698C	2
chr1:186316442	p.K1007N	2
chr1:186313130	p.S1824S	2
chr1:186321204	p.L791L	2
chr1:186315342	p.V1170V	2
chr1:186319500	p.S975S	2

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 TPR 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 TPR

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


AHCTF1,ARID4B,ASH1L,PRRC2C,SDE2,BROX,CDC73, CEP350,DHX9,FAM20B,GATAD2B,GON4L,HEATR1,IPO9, KLHL20,NUP133,RAB3GAP2,RBBP5,SMG7,TOR1AIP2,TPR	ASH1L,ASXL2,BOD1L1,ERCC6L2,CCNT1,ICE1,KIAA1109, KIDINS220,MYO9A,NIPBL,RAD50,RBM41,SETD2,SETX, TAF1,TPR,TRIP11,UBR5,UBXN7,USP34,ZNF354C

ARHGEF11,ARID4B,ARNT,ASH1L,PRRC2C,CEP350,DENND4B, DSTYK,GATAD2B,GON4L,INTS3,MTR,POGK,POGZ, RPRD2,SETDB1,SNX27,TP53BP2,TPR,WDR26,ZC3H11A	ALMS1,BAZ1B,BOD1L1,BPTF,HECTD4,CHD8,EP400, GIGYF2,HELZ,HERC1,HERC2,HUWE1,MGA,KMT2A, NSD1,TAF1,TPR,UBR5,USP34,VPS13B,YLPM1

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 TPR

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA36696; -.
Organism-specific databases	CTD	7175; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB02240	translocated promoter region, nuclear basket protein	experimental	N-{(1s)-4-[Bis(2-Chloroethyl)Amino]-1-Methylbutyl}-N-(6-Chloro-2-Methoxy-9-Acridinyl)Amine
DB03147	translocated promoter region, nuclear basket protein	experimental	Flavin-Adenine Dinucleotide
DB03470	translocated promoter region, nuclear basket protein	experimental	Trypanothione
DB04299	translocated promoter region, nuclear basket protein	experimental	Maleic Acid

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Cross referenced IDs for TPR

* 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