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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for EXOSC9 |
Basic gene info. | Gene symbol | EXOSC9 |
Gene name | exosome component 9 | |
Synonyms | PM/Scl-75|PMSCL1|RRP45|Rrp45p|p5|p6 | |
Cytomap | UCSC genome browser: 4q27 | |
Genomic location | chr4 :122722471-122738176 | |
Type of gene | protein-coding | |
RefGenes | NM_001034194.1, NM_005033.2, | |
Ensembl id | ENSG00000123737 | |
Description | P75 polymyositis-scleroderma overlap syndrome associated autoantigenP75 polymyositis-scleroderma overlap syndrome-associated autoantigenPMSCL autoantigen, 75kDautoantigen PM/Scl 1exosome complex component RRP45exosome complex exonuclease RRP45polymy | |
Modification date | 20141207 | |
dbXrefs | MIM : 606180 | |
HGNC : HGNC | ||
Ensembl : ENSG00000123737 | ||
HPRD : 07315 | ||
Vega : OTTHUMG00000128783 | ||
Protein | UniProt: Q06265 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_EXOSC9 | |
BioGPS: 5393 | ||
Gene Expression Atlas: ENSG00000123737 | ||
The Human Protein Atlas: ENSG00000123737 | ||
Pathway | NCI Pathway Interaction Database: EXOSC9 | |
KEGG: EXOSC9 | ||
REACTOME: EXOSC9 | ||
ConsensusPathDB | ||
Pathway Commons: EXOSC9 | ||
Metabolism | MetaCyc: EXOSC9 | |
HUMANCyc: EXOSC9 | ||
Regulation | Ensembl's Regulation: ENSG00000123737 | |
miRBase: chr4 :122,722,471-122,738,176 | ||
TargetScan: NM_001034194 | ||
cisRED: ENSG00000123737 | ||
Context | iHOP: EXOSC9 | |
cancer metabolism search in PubMed: EXOSC9 | ||
UCL Cancer Institute: EXOSC9 | ||
Assigned class in ccmGDB | B - This gene belongs to cancer gene. |
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Phenotypic Information for EXOSC9(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: EXOSC9 |
Familial Cancer Database: EXOSC9 |
* 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 | 606180; gene. |
Orphanet | |
Disease | KEGG Disease: EXOSC9 |
MedGen: EXOSC9 (Human Medical Genetics with Condition) | |
ClinVar: EXOSC9 | |
Phenotype | MGI: 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. |
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 EXOSC9 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=48) | (# total SNVs=13) |
(# total SNVs=4) | (# 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 |
chr4:122723894-122723894 | p.F78fs*23 | 3 |
chr4:122723012-122723012 | p.R33G | 3 |
chr4:122731249-122731249 | p.D245Y | 2 |
chr4:122734525-122734525 | p.P322S | 2 |
chr4:122737561-122737561 | p.E415E | 2 |
chr4:122737562-122737562 | p.M416V | 2 |
chr4:122728764-122728764 | p.F198V | 2 |
chr4:122735086-122735086 | p.W347S | 2 |
chr4:122722639-122722639 | p.E20D | 2 |
chr4:122723885-122723885 | p.E73V | 2 |
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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 | 3 | 2 | 9 | 1 |   | 1 |   | 2 | 1 |   | 1 | 1 |   |   |   | 3 | 5 |   | 8 |
# mutation | 4 | 3 | 2 | 9 | 1 |   | 1 |   | 2 | 1 |   | 1 | 1 |   |   |   | 3 | 5 |   | 9 |
nonsynonymous SNV | 4 | 3 | 2 | 8 | 1 |   | 1 |   | 1 | 1 |   |   | 1 |   |   |   | 2 | 3 |   | 8 |
synonymous SNV |   |   |   | 1 |   |   |   |   | 1 |   |   | 1 |   |   |   |   | 1 | 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 |
chr4:122735121 | p.E359K,EXOSC9 | 2 |
chr4:122724116 | p.D405H,EXOSC9 | 1 |
chr4:122731149 | p.I35F,EXOSC9 | 1 |
chr4:122722619 | p.F199Y,EXOSC9 | 1 |
chr4:122735086 | p.E211E,EXOSC9 | 1 |
chr4:122724120 | p.P408R,EXOSC9 | 1 |
chr4:122731151 | p.E49G,EXOSC9 | 1 |
chr4:122722621 | p.R212Q,EXOSC9 | 1 |
chr4:122725790 | p.P424S,EXOSC9 | 1 |
chr4:122731160 | p.F78L,EXOSC9 | 1 |
Other DBs for Point Mutations |
Copy 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 |
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 |
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 |
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 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 |
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