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 EXOSC9
Basic gene info.Gene symbolEXOSC9
Gene nameexosome component 9
SynonymsPM/Scl-75|PMSCL1|RRP45|Rrp45p|p5|p6
CytomapUCSC genome browser: 4q27
Genomic locationchr4 :122722471-122738176
Type of geneprotein-coding
RefGenesNM_001034194.1,
NM_005033.2,
Ensembl idENSG00000123737
DescriptionP75 polymyositis-scleroderma overlap syndrome associated autoantigenP75 polymyositis-scleroderma overlap syndrome-associated autoantigenPMSCL autoantigen, 75kDautoantigen PM/Scl 1exosome complex component RRP45exosome complex exonuclease RRP45polymy
Modification date20141207
dbXrefs MIM : 606180
HGNC : HGNC
Ensembl : ENSG00000123737
HPRD : 07315
Vega : OTTHUMG00000128783
ProteinUniProt: Q06265
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EXOSC9
BioGPS: 5393
Gene Expression Atlas: ENSG00000123737
The Human Protein Atlas: ENSG00000123737
PathwayNCI Pathway Interaction Database: EXOSC9
KEGG: EXOSC9
REACTOME: EXOSC9
ConsensusPathDB
Pathway Commons: EXOSC9
MetabolismMetaCyc: EXOSC9
HUMANCyc: EXOSC9
RegulationEnsembl's Regulation: ENSG00000123737
miRBase: chr4 :122,722,471-122,738,176
TargetScan: NM_001034194
cisRED: ENSG00000123737
ContextiHOP: EXOSC9
cancer metabolism search in PubMed: EXOSC9
UCL Cancer Institute: EXOSC9
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for EXOSC9(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EXOSC9
Familial Cancer Database: EXOSC9
* 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 606180; gene.
Orphanet
DiseaseKEGG Disease: EXOSC9
MedGen: EXOSC9 (Human Medical Genetics with Condition)
ClinVar: EXOSC9
PhenotypeMGI: EXOSC9 (International Mouse Phenotyping Consortium)
PhenomicDB: EXOSC9

Mutations for EXOSC9
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows EXOSC9 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=48)
Stat. for Synonymous SNVs
(# total SNVs=13)
Stat. for Deletions
(# total SNVs=4)
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
chr4:122723894-122723894p.F78fs*233
chr4:122723012-122723012p.R33G3
chr4:122737542-122737542p.S409*2
chr4:122731249-122731249p.D245Y2
chr4:122734525-122734525p.P322S2
chr4:122737561-122737561p.E415E2
chr4:122737562-122737562p.M416V2
chr4:122728764-122728764p.F198V2
chr4:122735086-122735086p.W347S2
chr4:122722639-122722639p.E20D2

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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
# sample43291 1 21 11   35 8
# mutation43291 1 21 11   35 9
nonsynonymous SNV43281 1 11  1   23 8
synonymous SNV   1    1  1    12 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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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
chr4:122735121p.E359K,EXOSC92
chr4:122723946p.T294T,EXOSC91
chr4:122728764p.R133H,EXOSC91
chr4:122722582p.A301V,EXOSC91
chr4:122734498p.N140H,EXOSC91
chr4:122724099p.E313K,EXOSC91
chr4:122728768p.M1I,EXOSC91
chr4:122722600p.T173A,EXOSC91
chr4:122735078p.E344D,EXOSC91
chr4:122724116p.S7S,EXOSC91

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 EXOSC9 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 EXOSC9

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

ANAPC10,CCNA2,CENPH,CISD2,EXOSC9,GAR1,H2AFZ,
HMGB2,HNRNPD,MAD2L1,CENPU,MND1,MRPL1,PSMC3IP,
PTTG1,SRSF2,SRSF3,SRSF7,SNRPD1,TROAP,UBE2T
BRIX1,C3orf33,CDK7,DNAJC2,DNTTIP2,EXOSC9,GTF2B,
H3F3B,INTS12,MED6,NAE1,NOP58,PRPF18,RCAN1,
TRMT10C,SRSF3,SRSF7,TAF11,TRA2B,YTHDF2,ZNF165

C4orf27,CCNA2,CCNB1,CDC20,CDC45,EXOSC9,H2AFZ,
HMGB2,LSM6,MAD2L1,CENPU,MND1,MRPS18C,NDUFC1,
PLK4,PSMA4,PSMC3IP,PTTG1,SNRPD1,SPATA5,TIPIN
BRIX1,DNAJC9,EIF4A1,EXOSC9,GTPBP4,KIAA0101,LTV1,
MAK16,NME1,NOP58,PA2G4,PNPT1,RANBP1,RFC3,
RFC4,SRSF3,SRSF7,SNRPD1,TFDP1,UTP6,VRK1
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 EXOSC9


There's no related Drug.
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Cross referenced IDs for EXOSC9
* 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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