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 TNPO1
Basic gene info.Gene symbolTNPO1
Gene nametransportin 1
SynonymsIPO2|KPNB2|MIP|MIP1|TRN
CytomapUCSC genome browser: 5q13.2
Genomic locationchr5 :72112417-72210215
Type of geneprotein-coding
RefGenesNM_002270.3,
NM_153188.2,
Ensembl idENSG00000083312
DescriptionM9 region interaction proteinimportin 2importin beta 2importin beta-2karyopherin (importin) beta 2karyopherin beta-2transportin-1
Modification date20141207
dbXrefs MIM : 602901
HGNC : HGNC
HPRD : 04210
ProteinUniProt: Q92973
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TNPO1
BioGPS: 3842
Gene Expression Atlas: ENSG00000083312
The Human Protein Atlas: ENSG00000083312
PathwayNCI Pathway Interaction Database: TNPO1
KEGG: TNPO1
REACTOME: TNPO1
ConsensusPathDB
Pathway Commons: TNPO1
MetabolismMetaCyc: TNPO1
HUMANCyc: TNPO1
RegulationEnsembl's Regulation: ENSG00000083312
miRBase: chr5 :72,112,417-72,210,215
TargetScan: NM_002270
cisRED: ENSG00000083312
ContextiHOP: TNPO1
cancer metabolism search in PubMed: TNPO1
UCL Cancer Institute: TNPO1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for TNPO1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TNPO1
Familial Cancer Database: TNPO1
* 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 602901; gene.
Orphanet
DiseaseKEGG Disease: TNPO1
MedGen: TNPO1 (Human Medical Genetics with Condition)
ClinVar: TNPO1
PhenotypeMGI: TNPO1 (International Mouse Phenotyping Consortium)
PhenomicDB: TNPO1

Mutations for TNPO1
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasTNPO1chr57212440572124425chr129869325698693276
pancreasTNPO1chr57216989472169914chr712044721204492
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 TNPO1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ338374TNPO1218657218509272185276ZFP106182259154270767442707751
BQ338570TNPO1215857218509272185255ZFP106154240154270767442707760
HM245392TNPO1110857214429472147146IKBKB10724884212959942146168
BE701928ZFP10615101154270767442707760TNPO19728157218509272185276
BQ338378ZFP10615101154270767442707760TNPO19728157218509272185276
BQ338569ZFP10614100154270767442707760TNPO19628057218509272185276

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 # sample1                
GAIN (# sample)                 
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=69)
Stat. for Synonymous SNVs
(# total SNVs=9)
Stat. for Deletions
(# total SNVs=8)
Stat. for Insertions
(# total SNVs=0)
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
chr5:72199545-72199545p.C836fs*456
chr5:72195908-72195908p.W797L3
chr5:72196828-72196828p.D806E3
chr5:72201211-72201211p.R883C3
chr5:72183988-72183988p.R455C2
chr5:72171523-72171523p.R246*2
chr5:72151675-72151675p.G86S2
chr5:72192969-72192969p.E769K2
chr5:72178958-72178958p.S342L2
chr5:72189511-72189511p.Q700H2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample33 19  1 22 422 138 11
# mutation33 19  1 22 422 1310 13
nonsynonymous SNV32 15  1 22 322  26 11
synonymous SNV 1 4       1   114 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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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
chr5:72201211p.R891C,TNPO13
chr5:72185728p.L549I,TNPO12
chr5:72151675p.E777K,TNPO12
chr5:72183988p.G94S,TNPO12
chr5:72192969p.R463C,TNPO12
chr5:72185719p.R879C,TNPO11
chr5:72161500p.A202A,TNPO11
chr5:72189471p.Y526C,TNPO11
chr5:72178909p.L721L,TNPO11
chr5:72195907p.L888L,TNPO11

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 TNPO1 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 TNPO1

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

AFF4,APC,ATRX,BDP1,C5orf24,CEP350,DNAJB14,
ERBB2IP,FCHO2,IPO11,MATR3,POLK,RBM27,SLC25A46,
SLC30A5,SMAD5,SRFBP1,TNPO1,TTC37,UHMK1,WDR36
ACAP2,ANKIB1,ATRX,BMPR2,CDC73,DCUN1D1,DICER1,
DNAJB14,EDEM3,INTS2,ITCH,TRAPPC8,KIAA1033,MED13,
MKLN1,OSBPL8,PIK3C2A,RAB11FIP2,RAB3GAP2,SEC24A,TNPO1

AGGF1,AGPS,BDP1,CHD1,DDX46,IPO11,KIF2A,
LNPEP,LYSMD3,MAN2A1,MATR3,MBLAC2,NLN,POLK,
PPIP5K2,RBM27,SKIV2L2,SLC30A5,TNPO1,UTP15,WDR36
AP3M1,CSRNP3,DAAM1,EIF5B,INTS2,KIF5B,LUC7L2,
MAN1A2,PHIP,PIK3C2A,PREPL,RBM26,ROCK1,NEMF,
SEC63,SREK1,SMARCA5,SUZ12,TNPO1,TOP2B,ZBTB11
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 TNPO1


There's no related Drug.
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Cross referenced IDs for TNPO1
* 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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