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 EXOSC7
Basic gene info.Gene symbolEXOSC7
Gene nameexosome component 7
SynonymsEAP1|RRP42|Rrp42p|hRrp42p|p8
CytomapUCSC genome browser: 3p21.31
Genomic locationchr3 :45017740-45052962
Type of geneprotein-coding
RefGenesNM_015004.3,
NR_023353.1,
Ensembl idENSG00000075914
Descriptionexosome complex component RRP42exosome complex exonuclease RRP42ribosomal RNA-processing protein 42
Modification date20141215
dbXrefs MIM : 606488
HGNC : HGNC
Ensembl : ENSG00000075914
HPRD : 09401
Vega : OTTHUMG00000133095
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EXOSC7
BioGPS: 23016
Gene Expression Atlas: ENSG00000075914
The Human Protein Atlas: ENSG00000075914
PathwayNCI Pathway Interaction Database: EXOSC7
KEGG: EXOSC7
REACTOME: EXOSC7
ConsensusPathDB
Pathway Commons: EXOSC7
MetabolismMetaCyc: EXOSC7
HUMANCyc: EXOSC7
RegulationEnsembl's Regulation: ENSG00000075914
miRBase: chr3 :45,017,740-45,052,962
TargetScan: NM_015004
cisRED: ENSG00000075914
ContextiHOP: EXOSC7
cancer metabolism search in PubMed: EXOSC7
UCL Cancer Institute: EXOSC7
Assigned class in ccmGDBC

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Phenotypic Information for EXOSC7(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_MRNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: EXOSC7
MedGen: EXOSC7 (Human Medical Genetics with Condition)
ClinVar: EXOSC7
PhenotypeMGI: EXOSC7 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryEXOSC7chr34502733645027356EXOSC7chr34502798045028000
prostateEXOSC7chr34502919245029192chr78223341482233414
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 EXOSC7 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CK430478EXOSC7150134501776145043101PRR4498633121099977710999912
CB241820EXOSC71824034505393845054160EXOSC724032134505283645053706

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=2

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check002.gifSomatic 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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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
chr3:45030671-45030671p.R33*2
chr3:45031088-45031088p.P69L2
chr3:45017782-45017782p.T5A2
chr3:45038599-45038599p.E92A1
chr3:45046872-45046872p.V194A1
chr3:45030632-45030632p.E20K1
chr3:45038655-45038655p.R111W1
chr3:45048921-45048921p.R209W1
chr3:45030635-45030635p.D21N1
chr3:45038681-45038681p.V119V1

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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
# sample 1 4  1  2 4    54 4
# mutation 1 4  1  2 5    54 4
nonsynonymous SNV 1 1  1  2 5    34 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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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
chr3:45038695p.D25G1
chr3:45052801p.R209W1
chr3:45030648p.R27C1
chr3:45038709p.S222S1
chr3:45052814p.E36K1
chr3:45030653p.S229S1
chr3:45038710p.S48S1
chr3:45052818p.V265V1
chr3:45030680p.F81L1
chr3:45038724p.H267L1

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 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

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

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
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 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



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