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 XPO1
Basic gene info.Gene symbolXPO1
Gene nameexportin 1
SynonymsCRM1|emb|exp1
CytomapUCSC genome browser: 2p15
Genomic locationchr2 :61705068-61765418
Type of geneprotein-coding
RefGenesNM_003400.3,
Ensembl idENSG00000082898
DescriptionCRM1, yeast, homologchromosome region maintenance 1 homologchromosome region maintenance 1 protein homologexportin 1 (CRM1 homolog, yeast)exportin-1exportin-1 (required for chromosome region maintenance)
Modification date20141222
dbXrefs MIM : 602559
HGNC : HGNC
Ensembl : ENSG00000082898
HPRD : 03975
Vega : OTTHUMG00000152316
ProteinUniProt: O14980
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_XPO1
BioGPS: 7514
Gene Expression Atlas: ENSG00000082898
The Human Protein Atlas: ENSG00000082898
PathwayNCI Pathway Interaction Database: XPO1
KEGG: XPO1
REACTOME: XPO1
ConsensusPathDB
Pathway Commons: XPO1
MetabolismMetaCyc: XPO1
HUMANCyc: XPO1
RegulationEnsembl's Regulation: ENSG00000082898
miRBase: chr2 :61,705,068-61,765,418
TargetScan: NM_003400
cisRED: ENSG00000082898
ContextiHOP: XPO1
cancer metabolism search in PubMed: XPO1
UCL Cancer Institute: XPO1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for XPO1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: XPO1
Familial Cancer Database: XPO1
* 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 CLL 6,

Therapeutic Vulnerabilities in Cancer7

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,
6 http://www.nature.com/nature/journal/v505/n7484/full/nature12912.html,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_MRNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM 602559; gene.
Orphanet
DiseaseKEGG Disease: XPO1
MedGen: XPO1 (Human Medical Genetics with Condition)
ClinVar: XPO1
PhenotypeMGI: XPO1 (International Mouse Phenotyping Consortium)
PhenomicDB: XPO1

Mutations for XPO1
* 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
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
haematopoietic_and_lymphoid_tissueXPO1chr26172688761726887XPO1chr26172688761726887
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 XPO1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA559883XPO116426172402861724091XPO16014826172268061724033
DB158037ZNF100186192191328621913371XPO18356026174977561764896
BG259252XPO11511226171533161715746XPO111072926170960861715358
BM462202XPO11610926170520561705298XPO19121326170506961705189
N53198XPO12336026171562561715962TRAPPC93543818141227840141227867
DB198554XPO1129426171379261714085XPO129162526171573161716065

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       1        
GAIN (# sample)1       1        
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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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=24

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=109)
Stat. for Synonymous SNVs
(# total SNVs=20)
Stat. for Deletions
(# total SNVs=2)
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
chr2:61719472-61719472p.E571K20
chr2:61715367-61715367p.R749Q6
chr2:61719471-61719471p.E571V4
chr2:61715726-61715726p.N735Y4
chr2:61726051-61726051p.?3
chr2:61722723-61722723p.R305Q3
chr2:61712909-61712909p.I834M2
chr2:61721179-61721179p.I365I2
chr2:61729443-61729443p.I102V2
chr2:61709610-61709610p.S959S2

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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=6

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample45113  4 81 721  45 18
# mutation44113  4 81 821  49 22
nonsynonymous SNV3318  3 81 62   25 17
synonymous SNV11 5  1    2 1  24 5
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
chr2:61719472p.E571K6
chr2:61715367p.R749Q4
chr2:61712950p.S959S2
chr2:61709610p.Q821E2
chr2:61722723p.R305Q2
chr2:61711133p.Q437E1
chr2:61721179p.L255L1
chr2:61726900p.V968V1
chr2:61719223p.P661P1
chr2:61760930p.N435N1

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 XPO1 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 XPO1

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

ASPM,BRCA2,CASC5,CEBPZ,CENPI,CKAP2L,ECT2,
MSH2,MSH6,NAA25,NUP155,RIF1,SGOL1,SGOL2,
SMC4,SMEK2,TMPO,TOPBP1,TTK,USP34,XPO1
FAM208A,C5orf51,FAM135A,FBXL4,GOPC,HERC4,IREB2,
UFL1,MORC3,ICE2,PMS1,SCAI,SENP7,SCAF11,
SMCHD1,SPAST,TIAL1,WDR36,XPO1,ZNF280D,ZNF770

ATAD5,BUB1,CCDC138,CEBPZ,DDX18,DNA2,FANCI,
FBXO5,KIAA1524,MSH2,NCAPH,PMS1,PNPT1,POLR2D,
PRPF40A,SGOL2,TMEM194A,TOPBP1,WDR43,WDR75,XPO1
CSE1L,DHX57,DNM1L,HAUS6,HNRNPA3,IARS,INTS2,
IPO9,LBR,LUC7L2,MSH6,NEDD1,NUP107,NUP205,
RBM26,RPGRIP1L,NEMF,TMEM194A,UBFD1,XPO1,XPO7
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 XPO1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB O14980; -.
ChemistryChEMBL CHEMBL5661; -.
Organism-specific databasesPharmGKB PA37418; -.
Organism-specific databasesCTD 7514; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00171exportin 1 (CRM1 homolog, yeast)approved; nutraceuticalAdenosine triphosphate
DB00864exportin 1 (CRM1 homolog, yeast)approved; investigationalTacrolimus


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Cross referenced IDs for XPO1
* 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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