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 EXOSC7

Basic gene info.	Gene symbol	EXOSC7
	Gene name	exosome component 7
	Synonyms	EAP1\|RRP42\|Rrp42p\|hRrp42p\|p8
	Cytomap	UCSC genome browser: 3p21.31
	Genomic location	chr3 :45017740-45052962
	Type of gene	protein-coding
	RefGenes	NM_015004.3, NR_023353.1,
	Ensembl id	ENSG00000075914
	Description	exosome complex component RRP42exosome complex exonuclease RRP42ribosomal RNA-processing protein 42
	Modification date	20141215
dbXrefs	MIM : 606488
	HGNC : HGNC
	Ensembl : ENSG00000075914
	HPRD : 09401
	Vega : OTTHUMG00000133095
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_EXOSC7
	BioGPS: 23016
	Gene Expression Atlas: ENSG00000075914
	The Human Protein Atlas: ENSG00000075914
Pathway	NCI Pathway Interaction Database: EXOSC7
	KEGG: EXOSC7
	REACTOME: EXOSC7
	ConsensusPathDB
	Pathway Commons: EXOSC7
Metabolism	MetaCyc: EXOSC7
	HUMANCyc: EXOSC7
Regulation	Ensembl's Regulation: ENSG00000075914
	miRBase: chr3 :45,017,740-45,052,962
	TargetScan: NM_015004
	cisRED: ENSG00000075914
Context	iHOP: EXOSC7
	cancer metabolism search in PubMed: EXOSC7
	UCL Cancer Institute: EXOSC7
Assigned class in ccmGDB	C

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Phenotypic Information for EXOSC7(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: EXOSC7
	Familial Cancer Database: EXOSC7

* 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM
Orphanet
Disease	KEGG Disease: EXOSC7
	MedGen: EXOSC7 (Human Medical Genetics with Condition)
	ClinVar: EXOSC7
Phenotype	MGI: EXOSC7 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: EXOSC7

Mutations for EXOSC7

* 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

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- 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
ovary	EXOSC7	chr3	45027336	45027356	EXOSC7	chr3	45027980	45028000
prostate	EXOSC7	chr3	45029192	45029192		chr7	82233414	82233414

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 EXOSC7 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
CK430478	EXOSC7	1	501	3	45017761	45043101	PRR4	498	633	12	10999777	10999912
CB241820	EXOSC7	18	240	3	45053938	45054160	EXOSC7	240	321	3	45052836	45053706

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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=15)	Stat. for Synonymous SNVs (# total SNVs=6)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	There's no inserted snv.

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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
chr3:45030671-45030671	p.R33*	2
chr3:45031088-45031088	p.P69L	2
chr3:45017782-45017782	p.T5A	2
chr3:45038599-45038599	p.E92A	1
chr3:45046872-45046872	p.V194A	1
chr3:45030632-45030632	p.E20K	1
chr3:45038655-45038655	p.R111W	1
chr3:45048921-45048921	p.R209W	1
chr3:45030635-45030635	p.D21N	1
chr3:45038681-45038681	p.V119V	1

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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=2

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		1		4			1			2		4					5	4		4
# mutation		1		4			1			2		5					5	4		4
nonsynonymous SNV		1		1			1			2		5					3	4		3
synonymous SNV				3													2			1

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
chr3:45038695	p.D25G	1
chr3:45052801	p.R209W	1
chr3:45030648	p.R27C	1
chr3:45038709	p.S222S	1
chr3:45052814	p.E36K	1
chr3:45030653	p.S229S	1
chr3:45038710	p.S48S	1
chr3:45052818	p.V265V	1
chr3:45030680	p.F81L	1
chr3:45038724	p.H267L	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 EXOSC7 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 EXOSC7

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


C19orf43,C19orf70,ELP6,CCDC12,TMA7,EXOSC7,GADD45GIP1, IFRD2,LOC440957,LSM7,MON1A,MRPL23,NDUFA11,PSMB6, RPSA,RPSAP58,RRP9,SS18L2,SURF2,TMEM42,UQCRC1	ADPRHL2,CCDC12,CHMP4B,DNTTIP1,EDF1,EEF1D,EIF3G, EXOSC7,FAU,LCMT1,LOC152217,NHP2L1,NT5C,OSGEP, POLR2F,PQBP1,RUVBL2,SDHAF1,SNRPD2,SURF2,ZNF622

UQCC3,SLIRP,UQCC2,CCDC12,CCDC58,TMA7,EXOSC7, GNL3,LSM3,MRPL17,MRPS25,NOP16,NUDT1,RPL14, RPUSD3,RRP9,SNRPF,SS18L2,THOC7,TKT,TRAIP	B9D1,HYPK,DCUN1D5,EBNA1BP2,EIF2B3,EIF3I,EXOSC7, EXOSC8,HAUS1,HNRNPC,MAGOHB,MORF4L2,NME1,NPM1, NPM3,PARK7,PPIL1,PRDX4,PRMT1,RAN,SNRPE

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 EXOSC7

There's no related Drug.

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Cross referenced IDs for EXOSC7

* 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