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 DIS3

Basic gene info.	Gene symbol	DIS3
	Gene name	DIS3 exosome endoribonuclease and 3'-5' exoribonuclease
	Synonyms	2810028N01Rik\|EXOSC11\|KIAA1008\|RRP44\|dis3p
	Cytomap	UCSC genome browser: 13q22.1
	Genomic location	chr13 :73329539-73356344
	Type of gene	protein-coding
	RefGenes	NM_001128226.2, NM_014953.4,
	Ensembl id	ENSG00000083520
	Description	DIS3 mitotic control homologexosome complex exonuclease RRP44exosome component 11mitotic control protein dis3 homologribosomal RNA-processing protein 44
	Modification date	20141207
dbXrefs	MIM : 607533
	HGNC : HGNC
	Ensembl : ENSG00000083520
	HPRD : 06338
Protein	UniProt: Q9Y2L1 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_DIS3
	BioGPS: 22894
	Gene Expression Atlas: ENSG00000083520
	The Human Protein Atlas: ENSG00000083520
Pathway	NCI Pathway Interaction Database: DIS3
	KEGG: DIS3
	REACTOME: DIS3
	ConsensusPathDB
	Pathway Commons: DIS3
Metabolism	MetaCyc: DIS3
	HUMANCyc: DIS3
Regulation	Ensembl's Regulation: ENSG00000083520
	miRBase: chr13 :73,329,539-73,356,344
	TargetScan: NM_001128226
	cisRED: ENSG00000083520
Context	iHOP: DIS3
	cancer metabolism search in PubMed: DIS3
	UCL Cancer Institute: DIS3
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of DIS3 in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM	607533; gene. 607533; gene.
Orphanet
Disease	KEGG Disease: DIS3
	MedGen: DIS3 (Human Medical Genetics with Condition)
	ClinVar: DIS3
Phenotype	MGI: DIS3 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	DIS3	chr13	73335378	73335398	DIS3	chr13	73338250	73338270

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows DIS3 related fusion information.

ID	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
AW993722	BORA	9	324	13	73329118	73329436	DIS3	316	621	13	73336895	73337200
BE813339	BORA	6	323	13	73329118	73329436	DIS3	315	566	13	73336950	73337200

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

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

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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=9

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Somatic 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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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
chr13:73346338-73346338	p.D488N	7
chr13:73347916-73347916	p.R382Q	6
chr13:73337650-73337650	p.R689Q	5
chr13:73352431-73352431	p.E158E	2
chr13:73345227-73345227	p.D554D	2
chr13:73350157-73350157	p.S243Y	2
chr13:73355005-73355005	p.T122I	2
chr13:73337661-73337661	p.H685H	2
chr13:73346337-73346337	p.D488A	2
chr13:73348145-73348145	p.G347E	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=4

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	2	4		13	2		5	1	4		3	12		1			7	5	1	11
# mutation	2	4		13	2		5	1	4		3	11		1			6	7	1	13
nonsynonymous SNV	1	3		9	2		4	1	4		3	8					5	4	1	7
synonymous SNV	1	1		4			1					3		1			1	3		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
chr13:73347916	p.R352Q,DIS3	4
chr13:73334716	p.R314T,DIS3	2
chr13:73346337	p.S885L,DIS3	2
chr13:73350130	p.D458G,DIS3	2
chr13:73346338	p.D458N,DIS3	2
chr13:73348154	p.R222T,DIS3	2
chr13:73345227	p.D524E,DIS3	2
chr13:73337680	p.E176K,DIS3	1
chr13:73349449	p.L737F,DIS3	1
chr13:73346014	p.R484K,DIS3	1

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 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

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


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

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 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