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 XRN1
Basic gene info.Gene symbolXRN1
Gene name5'-3' exoribonuclease 1
SynonymsSEP1
CytomapUCSC genome browser: 3q23
Genomic locationchr3 :142025448-142166853
Type of geneprotein-coding
RefGenesNM_001282857.1,
NM_001282859.1,NM_019001.4,NM_001042604.1,
Ensembl idENSG00000114127
Descriptionstrand-exchange protein 1 homolog
Modification date20141207
dbXrefs MIM : 607994
HGNC : HGNC
Ensembl : ENSG00000114127
HPRD : 10470
Vega : OTTHUMG00000159251
ProteinUniProt: Q8IZH2
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_XRN1
BioGPS: 54464
Gene Expression Atlas: ENSG00000114127
The Human Protein Atlas: ENSG00000114127
PathwayNCI Pathway Interaction Database: XRN1
KEGG: XRN1
REACTOME: XRN1
ConsensusPathDB
Pathway Commons: XRN1
MetabolismMetaCyc: XRN1
HUMANCyc: XRN1
RegulationEnsembl's Regulation: ENSG00000114127
miRBase: chr3 :142,025,448-142,166,853
TargetScan: NM_001282857
cisRED: ENSG00000114127
ContextiHOP: XRN1
cancer metabolism search in PubMed: XRN1
UCL Cancer Institute: XRN1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for XRN1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: XRN1
Familial Cancer Database: XRN1
* 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 607994; gene.
Orphanet
DiseaseKEGG Disease: XRN1
MedGen: XRN1 (Human Medical Genetics with Condition)
ClinVar: XRN1
PhenotypeMGI: XRN1 (International Mouse Phenotyping Consortium)
PhenomicDB: XRN1

Mutations for XRN1
* 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
ovaryXRN1chr3142089160142089180GK5chr3141894728141894748
ovaryXRN1chr3142122557142122577XRN1chr3142122614142122634
ovaryXRN1chr3142157079142157099XRN1chr3142157335142157355
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 XRN1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI871771XRN112783142029034142029311GNPTAB27247412102139379102139580
BE671625XRN112793142029034142029312GNPTAB27351812102139335102139580
DB537013NQO11297166974422169744518XRN12973313142053702142053736

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      1      
GAIN (# sample)1  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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=120)
Stat. for Synonymous SNVs
(# total SNVs=28)
Stat. for Deletions
(# total SNVs=6)
Stat. for Insertions
(# total SNVs=1)

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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
chr3:142089390-142089390p.C1047C6
chr3:142142427-142142427p.R229*3
chr3:142122802-142122802p.R638H3
chr3:142140334-142140334p.L340P3
chr3:142030643-142030643p.R1611fs*343
chr3:142142403-142142403p.R237W3
chr3:142137373-142137373p.T440M2
chr3:142089400-142089400p.R1044H2
chr3:142030480-142030480p.S1665F2
chr3:142031519-142031519p.H1580R2

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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
# sample36 23  9 73 1354  1012313
# mutation36 23  9 73 1354  1014315
nonsynonymous SNV24 16  7 63 1044  1014114
synonymous SNV12 7  2 1  31     21
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
chr3:142140334p.L340P,XRN13
chr3:142102234p.S1653Y,XRN12
chr3:142030480p.R638H,XRN12
chr3:142137373p.R842S,XRN12
chr3:142122802p.H1568R,XRN12
chr3:142031519p.T440M,XRN12
chr3:142151627p.L662L,XRN11
chr3:142031581p.V376V,XRN11
chr3:142094782p.F184C,XRN11
chr3:142137372p.G1510D,XRN11

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 XRN1 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 XRN1

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

ACAP2,ARMC8,ASXL2,ATR,BIRC6,DNAJC13,ELK4,
ITSN2,LRCH3,MAP3K2,MOB1A,OSBPL11,PIKFYVE,RASA2,
RIF1,SETX,STAG1,UBXN7,XRN1,ZBTB38,ZNF148
ANKRD12,ATG2B,ATRX,BIRC6,CHD9,DNAJB14,MED13,
MON2,PHC3,PTAR1,RAB3GAP2,RICTOR,RIF1,LTN1,
SCAF11,SMCHD1,SMG1,VPS13C,XRN1,ZFX,ZNF451

ACAP2,APOL6,BTN3A1,CD96,CYLD,DTX3L,GBP2,
GBP4,GPR171,IFIT2,JAK2,KIAA0226,OTUD4,PARP14,
PARP9,SAMD9L,SMCHD1,STAT2,TMEM140,UBR2,XRN1
APOL6,C18orf8,CCDC68,CLIC5,DTX3L,FGD6,GCC2,
HKDC1,KIF2A,MUC13,PARP14,PLEKHA7,PLS1,RNF19A,
SECTM1,SEMA6D,SMCHD1,UACA,UBR2,XRN1,ZNFX1
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 XRN1


There's no related Drug.
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Cross referenced IDs for XRN1
* 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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