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Gene: EXOSC9 |
Gene summary for EXOSC9 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | EXOSC9 | Gene ID | 5393 |
| Gene name | exosome component 9 | |
| Gene Alias | PCH1D | |
| Cytomap | 4q27 | |
| Gene Type | protein-coding | GO ID | GO:0000288 | UniProtAcc | Q06265 |
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Malignant transformation analysis |
| Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
| Malignant transformation involving gene list. |
| Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
| 5393 | EXOSC9 | LZE5T | Human | Esophagus | ESCC | 8.65e-04 | 2.12e-01 | 0.0514 |
| 5393 | EXOSC9 | LZE7T | Human | Esophagus | ESCC | 5.14e-05 | 1.63e-01 | 0.0667 |
| 5393 | EXOSC9 | LZE24T | Human | Esophagus | ESCC | 1.57e-03 | 9.55e-02 | 0.0596 |
| 5393 | EXOSC9 | LZE21T | Human | Esophagus | ESCC | 1.65e-04 | 4.21e-01 | 0.0655 |
| 5393 | EXOSC9 | P1T-E | Human | Esophagus | ESCC | 2.22e-06 | 1.91e-01 | 0.0875 |
| 5393 | EXOSC9 | P2T-E | Human | Esophagus | ESCC | 3.05e-25 | 5.11e-01 | 0.1177 |
| 5393 | EXOSC9 | P4T-E | Human | Esophagus | ESCC | 1.19e-15 | 3.52e-01 | 0.1323 |
| 5393 | EXOSC9 | P5T-E | Human | Esophagus | ESCC | 7.04e-21 | 2.71e-01 | 0.1327 |
| 5393 | EXOSC9 | P8T-E | Human | Esophagus | ESCC | 2.15e-05 | 1.99e-01 | 0.0889 |
| 5393 | EXOSC9 | P9T-E | Human | Esophagus | ESCC | 1.40e-06 | 1.27e-01 | 0.1131 |
| 5393 | EXOSC9 | P10T-E | Human | Esophagus | ESCC | 4.78e-10 | 1.76e-01 | 0.116 |
| 5393 | EXOSC9 | P11T-E | Human | Esophagus | ESCC | 1.28e-09 | 3.85e-01 | 0.1426 |
| 5393 | EXOSC9 | P12T-E | Human | Esophagus | ESCC | 4.73e-25 | 5.07e-01 | 0.1122 |
| 5393 | EXOSC9 | P15T-E | Human | Esophagus | ESCC | 1.05e-10 | 1.95e-01 | 0.1149 |
| 5393 | EXOSC9 | P16T-E | Human | Esophagus | ESCC | 1.14e-13 | 3.20e-01 | 0.1153 |
| 5393 | EXOSC9 | P17T-E | Human | Esophagus | ESCC | 1.28e-04 | 2.01e-01 | 0.1278 |
| 5393 | EXOSC9 | P19T-E | Human | Esophagus | ESCC | 1.04e-02 | 3.37e-01 | 0.1662 |
| 5393 | EXOSC9 | P20T-E | Human | Esophagus | ESCC | 2.13e-08 | 1.40e-01 | 0.1124 |
| 5393 | EXOSC9 | P21T-E | Human | Esophagus | ESCC | 3.93e-09 | 2.71e-01 | 0.1617 |
| 5393 | EXOSC9 | P22T-E | Human | Esophagus | ESCC | 8.23e-28 | 5.61e-01 | 0.1236 |
| Page: 1 2 3 4 5 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage. |
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Malignant transformation related pathway analysis |
| Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
| Figure of enriched GO biological processes. |
| Tissue | Disease Stage | Enriched GO biological Processes |
| Colorectum | AD |  |
| Colorectum | SER |  |
| Colorectum | MSS |  |
| Colorectum | MSI-H |  |
| Colorectum | FAP |  |
| ∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:0022613111 | Esophagus | ESCC | ribonucleoprotein complex biogenesis | 365/8552 | 463/18723 | 1.74e-49 | 1.11e-45 | 365 |
| GO:0042254111 | Esophagus | ESCC | ribosome biogenesis | 252/8552 | 299/18723 | 3.27e-44 | 1.04e-40 | 252 |
| GO:003447015 | Esophagus | ESCC | ncRNA processing | 300/8552 | 395/18723 | 3.09e-35 | 3.26e-32 | 300 |
| GO:0016072110 | Esophagus | ESCC | rRNA metabolic process | 197/8552 | 236/18723 | 1.31e-33 | 1.18e-30 | 197 |
| GO:0006364110 | Esophagus | ESCC | rRNA processing | 189/8552 | 225/18723 | 4.88e-33 | 3.87e-30 | 189 |
| GO:003466012 | Esophagus | ESCC | ncRNA metabolic process | 346/8552 | 485/18723 | 4.35e-31 | 2.51e-28 | 346 |
| GO:0009896111 | Esophagus | ESCC | positive regulation of catabolic process | 332/8552 | 492/18723 | 4.36e-23 | 9.22e-21 | 332 |
| GO:0031331111 | Esophagus | ESCC | positive regulation of cellular catabolic process | 292/8552 | 427/18723 | 8.67e-22 | 1.53e-19 | 292 |
| GO:1903311110 | Esophagus | ESCC | regulation of mRNA metabolic process | 210/8552 | 288/18723 | 3.25e-21 | 5.56e-19 | 210 |
| GO:0006401110 | Esophagus | ESCC | RNA catabolic process | 204/8552 | 278/18723 | 3.39e-21 | 5.66e-19 | 204 |
| GO:0034655110 | Esophagus | ESCC | nucleobase-containing compound catabolic process | 272/8552 | 407/18723 | 2.92e-18 | 2.90e-16 | 272 |
| GO:0006402110 | Esophagus | ESCC | mRNA catabolic process | 170/8552 | 232/18723 | 8.70e-18 | 8.00e-16 | 170 |
| GO:0006417111 | Esophagus | ESCC | regulation of translation | 304/8552 | 468/18723 | 1.53e-17 | 1.33e-15 | 304 |
| GO:004670018 | Esophagus | ESCC | heterocycle catabolic process | 286/8552 | 445/18723 | 1.12e-15 | 7.47e-14 | 286 |
| GO:004427019 | Esophagus | ESCC | cellular nitrogen compound catabolic process | 288/8552 | 451/18723 | 3.03e-15 | 1.79e-13 | 288 |
| GO:001943918 | Esophagus | ESCC | aromatic compound catabolic process | 295/8552 | 467/18723 | 1.09e-14 | 5.98e-13 | 295 |
| GO:190136118 | Esophagus | ESCC | organic cyclic compound catabolic process | 307/8552 | 495/18723 | 9.99e-14 | 4.80e-12 | 307 |
| GO:000095618 | Esophagus | ESCC | nuclear-transcribed mRNA catabolic process | 88/8552 | 112/18723 | 9.41e-13 | 4.14e-11 | 88 |
| GO:00905013 | Esophagus | ESCC | RNA phosphodiester bond hydrolysis | 110/8552 | 152/18723 | 1.95e-11 | 6.81e-10 | 110 |
| GO:0016049110 | Esophagus | ESCC | cell growth | 289/8552 | 482/18723 | 1.29e-10 | 3.77e-09 | 289 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0301824 | Esophagus | ESCC | RNA degradation | 62/4205 | 79/8465 | 1.18e-07 | 9.39e-07 | 4.81e-07 | 62 |
| hsa0301834 | Esophagus | ESCC | RNA degradation | 62/4205 | 79/8465 | 1.18e-07 | 9.39e-07 | 4.81e-07 | 62 |
| hsa030189 | Oral cavity | OSCC | RNA degradation | 59/3704 | 79/8465 | 2.05e-08 | 1.91e-07 | 9.70e-08 | 59 |
| hsa0301814 | Oral cavity | OSCC | RNA degradation | 59/3704 | 79/8465 | 2.05e-08 | 1.91e-07 | 9.70e-08 | 59 |
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Cell-cell communication analysis |
| Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
| Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
| Page: 1 |
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Single-cell gene regulatory network inference analysis |
| Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| ∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
| Page: 1 |
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Somatic mutation of malignant transformation related genes |
| Annotation of somatic variants for genes involved in malignant transformation |
| Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
| EXOSC9 | SNV | Missense_Mutation | c.1321N>T | p.Pro441Ser | p.P441S | Q06265 | protein_coding | tolerated_low_confidence(0.85) | benign(0.001) | TCGA-A2-A1G0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | SD | |
| EXOSC9 | SNV | Missense_Mutation | c.55N>A | p.Glu19Lys | p.E19K | Q06265 | protein_coding | tolerated(0.67) | benign(0.003) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| EXOSC9 | SNV | Missense_Mutation | rs761262917 | c.271G>A | p.Glu91Lys | p.E91K | Q06265 | protein_coding | deleterious(0) | possibly_damaging(0.838) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| EXOSC9 | SNV | Missense_Mutation | c.1100N>C | p.Ile367Thr | p.I367T | Q06265 | protein_coding | tolerated_low_confidence(0.98) | benign(0.001) | TCGA-D8-A1X6-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | tamoxiphen | SD | |
| EXOSC9 | SNV | Missense_Mutation | c.1274C>G | p.Pro425Arg | p.P425R | Q06265 | protein_coding | deleterious_low_confidence(0.02) | benign(0.232) | TCGA-E9-A1R2-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | taxotere | CR | |
| EXOSC9 | SNV | Missense_Mutation | novel | c.421N>T | p.His141Tyr | p.H141Y | Q06265 | protein_coding | deleterious(0.02) | possibly_damaging(0.637) | TCGA-OL-A5RZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | CR |
| EXOSC9 | SNV | Missense_Mutation | c.332G>C | p.Arg111Thr | p.R111T | Q06265 | protein_coding | deleterious(0.01) | probably_damaging(0.943) | TCGA-C5-A1M6-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD | |
| EXOSC9 | SNV | Missense_Mutation | c.1075G>A | p.Glu359Lys | p.E359K | Q06265 | protein_coding | tolerated_low_confidence(0.2) | benign(0.11) | TCGA-DR-A0ZM-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unspecific | Cisplatin | SD | |
| EXOSC9 | SNV | Missense_Mutation | rs201224124 | c.1303G>A | p.Ala435Thr | p.A435T | Q06265 | protein_coding | tolerated_low_confidence(0.48) | benign(0.036) | TCGA-AA-3710-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| EXOSC9 | SNV | Missense_Mutation | c.418A>C | p.Asn140His | p.N140H | Q06265 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-CA-6718-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
| Page: 1 2 3 4 5 6 |
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Related drugs of malignant transformation related genes |
| Identification of chemicals and drugs interact with genes involved in malignant transfromation |
| (DGIdb 4.0) |
| Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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