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Gene: RPS23 |
Gene summary for RPS23 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RPS23 | Gene ID | 6228 |
| Gene name | ribosomal protein S23 | |
| Gene Alias | BTDD | |
| Cytomap | 5q14.2 | |
| Gene Type | protein-coding | GO ID | GO:0002181 | UniProtAcc | A8K517 |
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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 |
| 6228 | RPS23 | GSM4909281 | Human | Breast | IDC | 4.14e-49 | -3.40e-01 | 0.21 |
| 6228 | RPS23 | GSM4909282 | Human | Breast | IDC | 6.06e-49 | -3.24e-01 | -0.0288 |
| 6228 | RPS23 | GSM4909285 | Human | Breast | IDC | 2.08e-24 | 2.03e-01 | 0.21 |
| 6228 | RPS23 | GSM4909287 | Human | Breast | IDC | 3.41e-42 | -4.64e-01 | 0.2057 |
| 6228 | RPS23 | GSM4909289 | Human | Breast | IDC | 7.90e-05 | -3.10e-01 | 0.1064 |
| 6228 | RPS23 | GSM4909290 | Human | Breast | IDC | 3.42e-36 | -3.59e-01 | 0.2096 |
| 6228 | RPS23 | GSM4909291 | Human | Breast | IDC | 1.83e-16 | -2.50e-01 | 0.1753 |
| 6228 | RPS23 | GSM4909292 | Human | Breast | IDC | 1.32e-16 | -6.04e-01 | 0.1236 |
| 6228 | RPS23 | GSM4909293 | Human | Breast | IDC | 3.08e-07 | -6.55e-02 | 0.1581 |
| 6228 | RPS23 | GSM4909297 | Human | Breast | IDC | 2.35e-04 | -1.79e-01 | 0.1517 |
| 6228 | RPS23 | GSM4909298 | Human | Breast | IDC | 1.56e-02 | 1.12e-01 | 0.1551 |
| 6228 | RPS23 | GSM4909304 | Human | Breast | IDC | 4.89e-18 | -1.30e-01 | 0.1636 |
| 6228 | RPS23 | GSM4909306 | Human | Breast | IDC | 2.66e-21 | -1.67e-01 | 0.1564 |
| 6228 | RPS23 | GSM4909312 | Human | Breast | IDC | 7.66e-03 | -6.23e-02 | 0.1552 |
| 6228 | RPS23 | GSM4909317 | Human | Breast | IDC | 2.53e-04 | -1.53e-01 | 0.1355 |
| 6228 | RPS23 | GSM4909319 | Human | Breast | IDC | 1.56e-31 | -5.01e-01 | 0.1563 |
| 6228 | RPS23 | brca1 | Human | Breast | Precancer | 2.40e-07 | -7.18e-02 | -0.0338 |
| 6228 | RPS23 | brca2 | Human | Breast | Precancer | 2.97e-28 | -1.86e-01 | -0.024 |
| 6228 | RPS23 | brca3 | Human | Breast | Precancer | 8.89e-20 | -1.32e-01 | -0.0263 |
| 6228 | RPS23 | brca10 | Human | Breast | Precancer | 1.99e-11 | -1.99e-01 | -0.0029 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:00021819 | Breast | Precancer | cytoplasmic translation | 80/1080 | 148/18723 | 1.59e-59 | 8.54e-56 | 80 |
| GO:00340635 | Breast | Precancer | stress granule assembly | 6/1080 | 26/18723 | 3.09e-03 | 2.62e-02 | 6 |
| GO:000218114 | Breast | IDC | cytoplasmic translation | 82/1434 | 148/18723 | 2.60e-52 | 1.48e-48 | 82 |
| GO:000218124 | Breast | DCIS | cytoplasmic translation | 82/1390 | 148/18723 | 2.21e-53 | 1.25e-49 | 82 |
| GO:000218110 | Cervix | CC | cytoplasmic translation | 96/2311 | 148/18723 | 4.87e-51 | 2.91e-47 | 96 |
| GO:000218115 | Cervix | HSIL_HPV | cytoplasmic translation | 86/737 | 148/18723 | 3.97e-82 | 1.91e-78 | 86 |
| GO:0002181 | Colorectum | AD | cytoplasmic translation | 109/3918 | 148/18723 | 3.40e-43 | 2.13e-39 | 109 |
| GO:00021812 | Colorectum | MSS | cytoplasmic translation | 108/3467 | 148/18723 | 1.78e-47 | 1.11e-43 | 108 |
| GO:00021814 | Colorectum | FAP | cytoplasmic translation | 76/2622 | 148/18723 | 3.31e-27 | 2.03e-23 | 76 |
| GO:0034063 | Colorectum | FAP | stress granule assembly | 10/2622 | 26/18723 | 1.77e-03 | 1.53e-02 | 10 |
| GO:000218116 | Endometrium | AEH | cytoplasmic translation | 104/2100 | 148/18723 | 1.01e-64 | 6.07e-61 | 104 |
| GO:000218117 | Endometrium | EEC | cytoplasmic translation | 104/2168 | 148/18723 | 2.53e-63 | 1.52e-59 | 104 |
| GO:000218127 | Esophagus | HGIN | cytoplasmic translation | 108/2587 | 148/18723 | 1.70e-60 | 1.02e-56 | 108 |
| GO:00340638 | Esophagus | HGIN | stress granule assembly | 10/2587 | 26/18723 | 1.60e-03 | 1.79e-02 | 10 |
| GO:0002181111 | Esophagus | ESCC | cytoplasmic translation | 135/8552 | 148/18723 | 4.17e-32 | 2.65e-29 | 135 |
| GO:003406315 | Esophagus | ESCC | stress granule assembly | 23/8552 | 26/18723 | 6.82e-06 | 6.90e-05 | 23 |
| GO:00021817 | Liver | NAFLD | cytoplasmic translation | 93/1882 | 148/18723 | 1.44e-55 | 8.41e-52 | 93 |
| GO:00340633 | Liver | NAFLD | stress granule assembly | 9/1882 | 26/18723 | 6.56e-04 | 8.50e-03 | 9 |
| GO:000218112 | Liver | Cirrhotic | cytoplasmic translation | 120/4634 | 148/18723 | 2.95e-47 | 1.85e-43 | 120 |
| GO:003406311 | Liver | Cirrhotic | stress granule assembly | 18/4634 | 26/18723 | 2.21e-06 | 4.10e-05 | 18 |
| Page: 1 2 3 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0301072 | Liver | Cyst | Ribosome | 70/339 | 167/8465 | 5.37e-55 | 1.55e-52 | 1.28e-52 | 70 |
| hsa0517172 | Liver | Cyst | Coronavirus disease - COVID-19 | 75/339 | 232/8465 | 2.97e-49 | 4.27e-47 | 3.53e-47 | 75 |
| hsa0517116 | Lung | IAC | Coronavirus disease - COVID-19 | 102/1053 | 232/8465 | 5.89e-34 | 1.91e-31 | 1.27e-31 | 102 |
| hsa0301016 | Lung | IAC | Ribosome | 76/1053 | 167/8465 | 1.18e-26 | 1.91e-24 | 1.27e-24 | 76 |
| hsa0517117 | Lung | IAC | Coronavirus disease - COVID-19 | 102/1053 | 232/8465 | 5.89e-34 | 1.91e-31 | 1.27e-31 | 102 |
| hsa0301017 | Lung | IAC | Ribosome | 76/1053 | 167/8465 | 1.18e-26 | 1.91e-24 | 1.27e-24 | 76 |
| hsa0517123 | Lung | AIS | Coronavirus disease - COVID-19 | 98/961 | 232/8465 | 2.82e-34 | 9.14e-32 | 5.85e-32 | 98 |
| hsa0301023 | Lung | AIS | Ribosome | 76/961 | 167/8465 | 2.61e-29 | 4.22e-27 | 2.70e-27 | 76 |
| hsa0517133 | Lung | AIS | Coronavirus disease - COVID-19 | 98/961 | 232/8465 | 2.82e-34 | 9.14e-32 | 5.85e-32 | 98 |
| hsa0301033 | Lung | AIS | Ribosome | 76/961 | 167/8465 | 2.61e-29 | 4.22e-27 | 2.70e-27 | 76 |
| hsa0301043 | Lung | AAH | Ribosome | 63/348 | 167/8465 | 3.21e-45 | 8.95e-43 | 7.19e-43 | 63 |
| hsa0517143 | Lung | AAH | Coronavirus disease - COVID-19 | 70/348 | 232/8465 | 9.07e-43 | 1.27e-40 | 1.02e-40 | 70 |
| hsa0301053 | Lung | AAH | Ribosome | 63/348 | 167/8465 | 3.21e-45 | 8.95e-43 | 7.19e-43 | 63 |
| hsa0517153 | Lung | AAH | Coronavirus disease - COVID-19 | 70/348 | 232/8465 | 9.07e-43 | 1.27e-40 | 1.02e-40 | 70 |
| hsa0301063 | Lung | MIAC | Ribosome | 70/507 | 167/8465 | 1.80e-42 | 5.24e-40 | 3.79e-40 | 70 |
| hsa0517163 | Lung | MIAC | Coronavirus disease - COVID-19 | 79/507 | 232/8465 | 4.83e-40 | 7.02e-38 | 5.08e-38 | 79 |
| hsa0301073 | Lung | MIAC | Ribosome | 70/507 | 167/8465 | 1.80e-42 | 5.24e-40 | 3.79e-40 | 70 |
| hsa0517173 | Lung | MIAC | Coronavirus disease - COVID-19 | 79/507 | 232/8465 | 4.83e-40 | 7.02e-38 | 5.08e-38 | 79 |
| hsa0301030 | Oral cavity | OSCC | Ribosome | 128/3704 | 167/8465 | 2.42e-18 | 1.62e-16 | 8.25e-17 | 128 |
| hsa0517130 | Oral cavity | OSCC | Coronavirus disease - COVID-19 | 156/3704 | 232/8465 | 2.30e-13 | 5.14e-12 | 2.62e-12 | 156 |
| Page: 1 2 3 4 5 6 |
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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 |
| RPS23 | SNV | Missense_Mutation | rs772924662 | c.98N>A | p.Gly33Asp | p.G33D | P62266 | protein_coding | tolerated(0.06) | possibly_damaging(0.903) | TCGA-AA-3672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| RPS23 | SNV | Missense_Mutation | c.233G>A | p.Gly78Asp | p.G78D | P62266 | protein_coding | deleterious(0.01) | benign(0.337) | TCGA-AA-3864-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| RPS23 | SNV | Missense_Mutation | c.116A>C | p.Asn39Thr | p.N39T | P62266 | protein_coding | tolerated(0.05) | benign(0.2) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| RPS23 | SNV | Missense_Mutation | c.253N>T | p.Val85Leu | p.V85L | P62266 | protein_coding | tolerated(0.08) | benign(0.169) | TCGA-AA-A01V-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| RPS23 | SNV | Missense_Mutation | novel | c.88N>A | p.Ala30Thr | p.A30T | P62266 | protein_coding | tolerated(0.23) | benign(0.13) | TCGA-AG-3878-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| RPS23 | SNV | Missense_Mutation | novel | c.260N>C | p.Asn87Thr | p.N87T | P62266 | protein_coding | tolerated(0.11) | benign(0.05) | TCGA-A5-A2K5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RPS23 | SNV | Missense_Mutation | novel | c.319N>T | p.Arg107Cys | p.R107C | P62266 | protein_coding | tolerated(0.09) | benign(0.077) | TCGA-EY-A548-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RPS23 | insertion | Frame_Shift_Ins | novel | c.162dupA | p.Val55SerfsTer4 | p.V55Sfs*4 | P62266 | protein_coding | TCGA-DD-A73G-01 | Liver | liver hepatocellular carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| RPS23 | SNV | Missense_Mutation | novel | c.407N>A | p.Gly136Asp | p.G136D | P62266 | protein_coding | deleterious(0.04) | benign(0.075) | TCGA-CN-6989-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | carboplatin | PD |
| RPS23 | insertion | Frame_Shift_Ins | novel | c.322_323insTAAAAAAAGT | p.Lys108IlefsTer10 | p.K108Ifs*10 | P62266 | protein_coding | TCGA-HD-8635-01 | Oral cavity | head & neck squamous cell carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| Page: 1 2 |
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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 |
| Page: 1 |
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