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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for EXOSC8 |
Basic gene info. | Gene symbol | EXOSC8 |
Gene name | exosome component 8 | |
Synonyms | CIP3|EAP2|OIP2|PCH1C|RRP43|Rrp43p|bA421P11.3|p9 | |
Cytomap | UCSC genome browser: 13q13.1 | |
Genomic location | chr13 :37574677-37583751 | |
Type of gene | protein-coding | |
RefGenes | NM_181503.2, | |
Ensembl id | ENSG00000120699 | |
Description | CBP-interacting protein 3OIP-2Opa interacting protein 2exosome complex component RRP43exosome complex exonuclease RRP43opa-interacting protein 2ribosomal RNA-processing protein 43 | |
Modification date | 20141207 | |
dbXrefs | MIM : 606019 | |
HGNC : HGNC | ||
Ensembl : ENSG00000120699 | ||
HPRD : 09351 | ||
Vega : OTTHUMG00000016742 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_EXOSC8 | |
BioGPS: 11340 | ||
Gene Expression Atlas: ENSG00000120699 | ||
The Human Protein Atlas: ENSG00000120699 | ||
Pathway | NCI Pathway Interaction Database: EXOSC8 | |
KEGG: EXOSC8 | ||
REACTOME: EXOSC8 | ||
ConsensusPathDB | ||
Pathway Commons: EXOSC8 | ||
Metabolism | MetaCyc: EXOSC8 | |
HUMANCyc: EXOSC8 | ||
Regulation | Ensembl's Regulation: ENSG00000120699 | |
miRBase: chr13 :37,574,677-37,583,751 | ||
TargetScan: NM_181503 | ||
cisRED: ENSG00000120699 | ||
Context | iHOP: EXOSC8 | |
cancer metabolism search in PubMed: EXOSC8 | ||
UCL Cancer Institute: EXOSC8 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for EXOSC8(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: EXOSC8 |
Familial Cancer Database: EXOSC8 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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: EXOSC8 |
MedGen: EXOSC8 (Human Medical Genetics with Condition) | |
ClinVar: EXOSC8 | |
Phenotype | MGI: EXOSC8 (International Mouse Phenotyping Consortium) |
PhenomicDB: EXOSC8 |
Mutations for EXOSC8 |
* 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 |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows EXOSC8 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 |
Other DBs for Structural Variants |
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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 |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=18) | (# total SNVs=5) |
(# total SNVs=0) | (# total SNVs=0) |
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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 |
chr13:37581138-37581138 | p.L139L | 3 |
chr13:37577117-37577117 | p.N55N | 2 |
chr13:37582255-37582255 | p.K183N | 1 |
chr13:37580087-37580087 | p.S90L | 1 |
chr13:37582284-37582284 | p.P193L | 1 |
chr13:37580090-37580090 | p.S91L | 1 |
chr13:37582924-37582924 | p.T223P | 1 |
chr13:37580102-37580102 | p.S95C | 1 |
chr13:37582930-37582930 | p.V225L | 1 |
chr13:37576630-37576630 | p.E20D | 1 |
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SNV Counts per Each Loci in TCGA data |
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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 |   |   |   | 4 | 1 |   |   |   | 3 |   |   |   |   |   |   |   | 2 | 2 |   | 1 |
# mutation |   |   |   | 4 | 1 |   |   |   | 4 |   |   |   |   |   |   |   | 2 | 2 |   | 1 |
nonsynonymous SNV |   |   |   | 3 | 1 |   |   |   | 4 |   |   |   |   |   |   |   | 1 | 2 |   | 1 |
synonymous SNV |   |   |   | 1 |   |   |   |   |   |   |   |   |   |   |   |   | 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 |
chr13:37581124 | p.V225L | 1 |
chr13:37581194 | p.C233Y | 1 |
chr13:37582255 | p.V8M | 1 |
chr13:37576414 | p.K52R | 1 |
chr13:37582284 | p.N55K | 1 |
chr13:37577107 | p.A68P | 1 |
chr13:37582930 | p.Y78Y | 1 |
chr13:37577117 | p.S90L | 1 |
chr13:37582955 | p.S95C | 1 |
chr13:37578662 | p.Q120P | 1 |
Other DBs for Point Mutations |
Copy Number for EXOSC8 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 EXOSC8 |
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. |
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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 |
ALG5,TEX30,EXOSC8,SUPT20H,GSDMA,GTF3A,HMGB1, LRAT,MITD1,MRPS31,POLR1D,POMP,RFC3,RFXAP, RNASEH2B,SRSF3,SKA3,SNRPG,SPG20,TPRKB,UCHL3 | SFR1,TEX30,METTL23,C18orf21,C4orf27,C8orf59,COMMD6, COX16,EIF3M,EXOSC8,GNRHR2,HMGN3,LIPT1,LSM5, RBM22,RPF1,RPL22L1,RSL24D1,SS18L2,TM2D3,TPRKB |
ALG5,TEX30,BORA,MZT1,DLEU1,EBPL,ESD, EXOSC8,GTF2F2,HMGB1,GPALPP1,MED4,MRPS31,NUFIP1, PCID2,POMP,RFC3,RNASEH2B,SKA3,TGDS,UCHL3 | CDC123,COPS3,ENOPH1,EXOSC8,GEMIN6,HAUS1,MAGOHB, MRPL52,NPM1,NUP37,PFDN6,POLR2G,PPIH,PRDX4, PSMD14,RAN,RPL26L1,SNRNP40,SNRPE,SSBP1,TOMM5 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for EXOSC8 |
There's no related Drug. |
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Cross referenced IDs for EXOSC8 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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