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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for EXOSC1 |
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Phenotypic Information for EXOSC1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: EXOSC1 |
Familial Cancer Database: EXOSC1 |
* 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: EXOSC1 |
MedGen: EXOSC1 (Human Medical Genetics with Condition) | |
ClinVar: EXOSC1 | |
Phenotype | MGI: EXOSC1 (International Mouse Phenotyping Consortium) |
PhenomicDB: EXOSC1 |
Mutations for EXOSC1 |
* 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 | Top |
- 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 |
There's no intra-chromosomal structural variation. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | EXOSC1 | chr10 | 99205013 | 99205033 | COL5A1 | chr9 | 137670326 | 137670346 |
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 EXOSC1 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 |
BF361687 | EXOSC1 | 1 | 112 | 10 | 99195675 | 99195786 | EXOSC1 | 107 | 228 | 10 | 99196384 | 99196505 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample |   |   |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   | |||
GAIN (# sample) |   |   |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract) |
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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=4) | (# total SNVs=3) |
(# 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 |
chr10:99205521-99205521 | p.G39S | 2 |
chr10:99200940-99200940 | p.R100Q | 1 |
chr10:99200974-99200974 | p.Y89H | 1 |
chr10:99200984-99200984 | p.V85V | 1 |
chr10:99203015-99203015 | p.V67V | 1 |
chr10:99196219-99196219 | p.E191K | 1 |
chr10:99196230-99196230 | p.R187Q | 1 |
chr10:99205554-99205554 | p.T28P | 1 |
chr10:99196244-99196244 | p.F182L | 1 |
chr10:99205605-99205605 | p.? | 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 |   |   | 1 |   |   |   | 2 |   |   |   |   | 1 | 1 |   |   |   | 2 | 3 |   | 2 |
# mutation |   |   | 1 |   |   |   | 2 |   |   |   |   | 3 | 1 |   |   |   | 2 | 3 |   | 2 |
nonsynonymous SNV |   |   | 1 |   |   |   | 1 |   |   |   |   | 2 | 1 |   |   |   | 1 | 2 |   |   |
synonymous SNV |   |   |   |   |   |   | 1 |   |   |   |   | 1 |   |   |   |   | 1 | 1 |   | 2 |
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 |
chr10:99196230 | p.R187L | 2 |
chr10:99198446 | p.V67V | 1 |
chr10:99200984 | p.R57T | 1 |
chr10:99202994 | p.V5V | 1 |
chr10:99203015 | p.E191K | 1 |
chr10:99196219 | p.F182L | 1 |
chr10:99203046 | p.H157Y | 1 |
chr10:99205728 | p.A156A | 1 |
chr10:99196244 | p.N149N | 1 |
chr10:99196960 | p.S134S | 1 |
Other DBs for Point Mutations |
Copy Number for EXOSC1 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 EXOSC1 |
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 |
ATP5G2,C12orf45,C19orf43,CUEDC2,EXOSC1,GSTO1,HIGD2A, KRTCAP2,MRPL43,MTX1,NDUFB8,OST4,POLR2J,SFXN4, SLC25A28,SNRPA,TAF10,TRAPPC1,TXNDC17,USMG5,ZDHHC16 | BUD31,C17orf49,C19orf43,WDR83OS,COA3,CSNK2B,EXOSC1, JTB,LSM2,MDP1,MRPS21,NSMCE1,PSENEN,SF3B5, SRP14,SSBP1,TMEM219,TOMM6,TRMT112,UBA52,UXT |
ATP5L,FAM204A,C19orf53,CCDC58,CWF19L1,DPY30,EXOSC1, GEMIN6,GLRX3,MRPL43,NDUFB8,NPM3,PCGF6,RPP30, RPS13,RPS15A,SFXN4,SNRPC,SNRPE,SNRPG,USMG5 | ANAPC11,ASNA1,ATP6V1F,TMEM258,ELP6,COPZ1,EXOSC1, FAU,LSM7,OSGEP,OST4,POLR2G,RPL19,RPL27A, RPL35,RPS16,SERF2,SNRPC,SNRPD2,SSR2,ZNF511 |
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 EXOSC1 |
There's no related Drug. |
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Cross referenced IDs for EXOSC1 |
* 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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