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 DIS3
Basic gene info.Gene symbolDIS3
Gene nameDIS3 exosome endoribonuclease and 3'-5' exoribonuclease
Synonyms2810028N01Rik|EXOSC11|KIAA1008|RRP44|dis3p
CytomapUCSC genome browser: 13q22.1
Genomic locationchr13 :73329539-73356344
Type of geneprotein-coding
RefGenesNM_001128226.2,
NM_014953.4,
Ensembl idENSG00000083520
DescriptionDIS3 mitotic control homologexosome complex exonuclease RRP44exosome component 11mitotic control protein dis3 homologribosomal RNA-processing protein 44
Modification date20141207
dbXrefs MIM : 607533
HGNC : HGNC
Ensembl : ENSG00000083520
HPRD : 06338
ProteinUniProt: Q9Y2L1
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DIS3
BioGPS: 22894
Gene Expression Atlas: ENSG00000083520
The Human Protein Atlas: ENSG00000083520
PathwayNCI Pathway Interaction Database: DIS3
KEGG: DIS3
REACTOME: DIS3
ConsensusPathDB
Pathway Commons: DIS3
MetabolismMetaCyc: DIS3
HUMANCyc: DIS3
RegulationEnsembl's Regulation: ENSG00000083520
miRBase: chr13 :73,329,539-73,356,344
TargetScan: NM_001128226
cisRED: ENSG00000083520
ContextiHOP: DIS3
cancer metabolism search in PubMed: DIS3
UCL Cancer Institute: DIS3
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of DIS3 in cancer cell metabolism1. Rose AE, Poliseno L, Wang J, Clark M, Pearlman A, et al. (2011) Integrative genomics identifies molecular alterations that challenge the linear model of melanoma progression. Cancer Res 71: 2561-2571. doi: 10.1158/0008-5472.CAN-10-2958. pmid: 3070783. go to article
2. Murakami H, Goto DB, Toda T, Chen ES, Grewal SI, et al. (2007) Ribonuclease activity of Dis3 is required for mitotic progression and provides a possible link between heterochromatin and kinetochore function. PLoS One 2: e317. doi: 10.1371/journal.pone.0000317. pmid: 1820850. go to article
3. de Groen FL, Krijgsman O, Tijssen M, Vriend LE, Ylstra B, et al. (2014) Gene-dosage dependent overexpression at the 13q amplicon identifies DIS3 as candidate oncogene in colorectal cancer progression. Genes Chromosomes Cancer 53: 339-348. doi: 10.1002/gcc.22144. go to article
4. Astuti D, Morris MR, Cooper WN, Staals RH, Wake NC, et al. (2012) Germline mutations in DIS3L2 cause the Perlman syndrome of overgrowth and Wilms tumor susceptibility. Nat Genet 44: 277-284. doi: 10.1038/ng.1071. go to article

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Phenotypic Information for DIS3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: DIS3
Familial Cancer Database: DIS3
* 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 MM 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 607533; gene.
607533; gene.
Orphanet
DiseaseKEGG Disease: DIS3
MedGen: DIS3 (Human Medical Genetics with Condition)
ClinVar: DIS3
PhenotypeMGI: DIS3 (International Mouse Phenotyping Consortium)
PhenomicDB: DIS3

Mutations for DIS3
* 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
pancreasDIS3chr137333537873335398DIS3chr137333825073338270
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 DIS3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW993722BORA9324137332911873329436DIS3316621137333689573337200
BE813339BORA6323137332911873329436DIS3315566137333695073337200

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
There's no copy number variation information in COSMIC data for this gene.

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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=9

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=88)
Stat. for Synonymous SNVs
(# total SNVs=24)
Stat. for Deletions
(# total SNVs=2)
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
chr13:73346338-73346338p.D488N7
chr13:73347916-73347916p.R382Q6
chr13:73337650-73337650p.R689Q5
chr13:73335846-73335846p.L817V2
chr13:73336102-73336102p.L767F2
chr13:73349502-73349502p.Q278H2
chr13:73345997-73345997p.R514M2
chr13:73350083-73350083p.D268N2
chr13:73352431-73352431p.E158E2
chr13:73345227-73345227p.D554D2

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample24 132 514 312 1  75111
# mutation24 132 514 311 1  67113
nonsynonymous SNV13 92 414 38    5417
synonymous SNV11 4  1    3 1  13 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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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
chr13:73347916p.R352Q,DIS34
chr13:73345227p.R222T,DIS32
chr13:73334716p.D524E,DIS32
chr13:73346337p.R314T,DIS32
chr13:73350130p.S885L,DIS32
chr13:73346338p.D458G,DIS32
chr13:73348154p.D458N,DIS32
chr13:73348179p.K424R,DIS31
chr13:73336150p.D238N,DIS31
chr13:73350163p.A803T,DIS31

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 DIS3 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 DIS3

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

ABHD13,BORA,MZT1,COG6,CUL4A,DIS3,GPR180,
GPALPP1,KPNA3,MTMR6,NDFIP2,NUPL1,PIBF1,RBM26,
RNF219,SUCLA2,TM9SF2,TPP2,XPO4,ZDHHC20,CHAMP1
ANKRD13C,APPBP2,ATRX,C5orf51,CAPN7,CEP120,DCP1A,
DENND4C,DIS3,HACE1,ITCH,LRRC58,ICE2,NMD3,
PJA2,PKN2,RAB3GAP2,UBE4A,USP8,VPS54,ZDHHC17

BORA,CUL4A,DIS3,ELF1,SUPT20H,FBXL3,INTS6,
IPO5,GPALPP1,KPNA3,MRPS31,N4BP2L2,PIBF1,RBM26,
RNF219,TM9SF2,TPP2,TUBGCP3,UFM1,UTP14C,WBP4
CAND1,CWC22,DIS3,EYA3,OTULIN,FUBP1,HNRNPR,
KIAA1033,MTDH,NAA50,NUP160,PRPF40A,RAB3GAP2,RBM12,
RBM27,SEC23IP,SMARCA5,STT3B,SUZ12,TAF2,UBE3A
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 DIS3


There's no related Drug.
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Cross referenced IDs for DIS3
* 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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