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Gene: RPS5 |
Gene summary for RPS5 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RPS5 | Gene ID | 6193 |
| Gene name | ribosomal protein S5 | |
| Gene Alias | S5 | |
| Cytomap | 19q13.43 | |
| Gene Type | protein-coding | GO ID | GO:0000028 | UniProtAcc | A0A024R4Q8 |
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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 |
| 6193 | RPS5 | RNA-P17T-P17T-8 | Human | Lung | IAC | 1.41e-02 | -1.90e-01 | 0.3329 |
| 6193 | RPS5 | RNA-P25T1-P25T1-1 | Human | Lung | AIS | 1.29e-16 | 2.09e-02 | -0.2116 |
| 6193 | RPS5 | RNA-P25T1-P25T1-2 | Human | Lung | AIS | 1.05e-06 | -2.54e-02 | -0.1941 |
| 6193 | RPS5 | RNA-P25T1-P25T1-3 | Human | Lung | AIS | 2.64e-08 | -1.72e-01 | -0.2107 |
| 6193 | RPS5 | RNA-P25T1-P25T1-4 | Human | Lung | AIS | 3.99e-13 | 4.75e-02 | -0.2119 |
| 6193 | RPS5 | RNA-P3T-P3T-1 | Human | Lung | IAC | 5.82e-07 | -6.17e-01 | 0.1829 |
| 6193 | RPS5 | RNA-P3T-P3T-2 | Human | Lung | IAC | 8.83e-03 | -5.81e-01 | 0.1835 |
| 6193 | RPS5 | RNA-P3T-P3T-4 | Human | Lung | IAC | 3.83e-04 | -5.72e-01 | 0.1859 |
| 6193 | RPS5 | RNA-P6T1-P6T1-4 | Human | Lung | MIAC | 5.98e-04 | -4.68e-01 | -0.0263 |
| 6193 | RPS5 | RNA-P6T2-P6T2-1 | Human | Lung | IAC | 4.31e-16 | -3.86e-01 | -0.0166 |
| 6193 | RPS5 | RNA-P6T2-P6T2-2 | Human | Lung | IAC | 1.49e-20 | -5.40e-01 | -0.0132 |
| 6193 | RPS5 | RNA-P6T2-P6T2-3 | Human | Lung | IAC | 2.50e-26 | -4.60e-01 | -0.013 |
| 6193 | RPS5 | RNA-P6T2-P6T2-4 | Human | Lung | IAC | 5.75e-16 | -5.19e-01 | -0.0121 |
| 6193 | RPS5 | RNA-P7T1-P7T1-1 | Human | Lung | AIS | 6.81e-09 | -9.75e-02 | -0.0961 |
| 6193 | RPS5 | RNA-P7T1-P7T1-2 | Human | Lung | AIS | 8.16e-07 | -2.37e-01 | -0.0876 |
| 6193 | RPS5 | RNA-P7T1-P7T1-3 | Human | Lung | AIS | 2.46e-08 | -4.58e-03 | -0.0822 |
| 6193 | RPS5 | RNA-P7T1-P7T1-4 | Human | Lung | AIS | 1.49e-11 | -3.02e-02 | -0.0809 |
| 6193 | RPS5 | C04 | Human | Oral cavity | OSCC | 1.07e-64 | 4.91e+00 | 0.2633 |
| 6193 | RPS5 | C21 | Human | Oral cavity | OSCC | 4.40e-66 | 4.37e+00 | 0.2678 |
| 6193 | RPS5 | C30 | Human | Oral cavity | OSCC | 3.54e-105 | 5.35e+00 | 0.3055 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 |
| 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 | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| 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:00226139 | Breast | Precancer | ribonucleoprotein complex biogenesis | 79/1080 | 463/18723 | 2.11e-18 | 1.03e-15 | 79 |
| GO:00718269 | Breast | Precancer | ribonucleoprotein complex subunit organization | 48/1080 | 227/18723 | 2.68e-15 | 8.45e-13 | 48 |
| GO:00226189 | Breast | Precancer | ribonucleoprotein complex assembly | 47/1080 | 220/18723 | 3.47e-15 | 1.03e-12 | 47 |
| GO:00422549 | Breast | Precancer | ribosome biogenesis | 52/1080 | 299/18723 | 7.35e-13 | 1.51e-10 | 52 |
| GO:00064138 | Breast | Precancer | translational initiation | 30/1080 | 118/18723 | 3.23e-12 | 5.58e-10 | 30 |
| GO:00422559 | Breast | Precancer | ribosome assembly | 21/1080 | 61/18723 | 1.06e-11 | 1.53e-09 | 21 |
| GO:00422749 | Breast | Precancer | ribosomal small subunit biogenesis | 21/1080 | 73/18723 | 4.84e-10 | 4.39e-08 | 21 |
| GO:00000289 | Breast | Precancer | ribosomal small subunit assembly | 10/1080 | 19/18723 | 2.24e-08 | 1.50e-06 | 10 |
| GO:000218114 | Breast | IDC | cytoplasmic translation | 82/1434 | 148/18723 | 2.60e-52 | 1.48e-48 | 82 |
| GO:002261314 | Breast | IDC | ribonucleoprotein complex biogenesis | 83/1434 | 463/18723 | 2.01e-13 | 5.20e-11 | 83 |
| GO:007182614 | Breast | IDC | ribonucleoprotein complex subunit organization | 52/1434 | 227/18723 | 5.18e-13 | 1.21e-10 | 52 |
| GO:002261814 | Breast | IDC | ribonucleoprotein complex assembly | 51/1434 | 220/18723 | 5.32e-13 | 1.21e-10 | 51 |
| GO:000641313 | Breast | IDC | translational initiation | 31/1434 | 118/18723 | 7.29e-10 | 7.52e-08 | 31 |
| GO:004225514 | Breast | IDC | ribosome assembly | 21/1434 | 61/18723 | 1.98e-09 | 1.76e-07 | 21 |
| GO:004225414 | Breast | IDC | ribosome biogenesis | 52/1434 | 299/18723 | 1.90e-08 | 1.32e-06 | 52 |
| GO:004227414 | Breast | IDC | ribosomal small subunit biogenesis | 21/1434 | 73/18723 | 7.23e-08 | 4.42e-06 | 21 |
| GO:000002814 | Breast | IDC | ribosomal small subunit assembly | 10/1434 | 19/18723 | 3.27e-07 | 1.69e-05 | 10 |
| GO:000218124 | Breast | DCIS | cytoplasmic translation | 82/1390 | 148/18723 | 2.21e-53 | 1.25e-49 | 82 |
| GO:002261324 | Breast | DCIS | ribonucleoprotein complex biogenesis | 83/1390 | 463/18723 | 3.65e-14 | 1.09e-11 | 83 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0301018 | Breast | Precancer | Ribosome | 80/684 | 167/8465 | 7.33e-44 | 2.32e-41 | 1.77e-41 | 80 |
| hsa0517118 | Breast | Precancer | Coronavirus disease - COVID-19 | 81/684 | 232/8465 | 3.74e-32 | 2.36e-30 | 1.81e-30 | 81 |
| hsa0301019 | Breast | Precancer | Ribosome | 80/684 | 167/8465 | 7.33e-44 | 2.32e-41 | 1.77e-41 | 80 |
| hsa0517119 | Breast | Precancer | Coronavirus disease - COVID-19 | 81/684 | 232/8465 | 3.74e-32 | 2.36e-30 | 1.81e-30 | 81 |
| hsa0301024 | Breast | IDC | Ribosome | 83/867 | 167/8465 | 6.07e-39 | 9.87e-37 | 7.38e-37 | 83 |
| hsa0517124 | Breast | IDC | Coronavirus disease - COVID-19 | 86/867 | 232/8465 | 1.50e-28 | 9.72e-27 | 7.27e-27 | 86 |
| hsa0301034 | Breast | IDC | Ribosome | 83/867 | 167/8465 | 6.07e-39 | 9.87e-37 | 7.38e-37 | 83 |
| hsa0517134 | Breast | IDC | Coronavirus disease - COVID-19 | 86/867 | 232/8465 | 1.50e-28 | 9.72e-27 | 7.27e-27 | 86 |
| hsa0301044 | Breast | DCIS | Ribosome | 82/846 | 167/8465 | 8.69e-39 | 1.40e-36 | 1.03e-36 | 82 |
| hsa0517144 | Breast | DCIS | Coronavirus disease - COVID-19 | 86/846 | 232/8465 | 2.42e-29 | 1.56e-27 | 1.15e-27 | 86 |
| hsa0301054 | Breast | DCIS | Ribosome | 82/846 | 167/8465 | 8.69e-39 | 1.40e-36 | 1.03e-36 | 82 |
| hsa0517154 | Breast | DCIS | Coronavirus disease - COVID-19 | 86/846 | 232/8465 | 2.42e-29 | 1.56e-27 | 1.15e-27 | 86 |
| hsa0517120 | Cervix | CC | Coronavirus disease - COVID-19 | 111/1267 | 232/8465 | 1.82e-33 | 5.90e-31 | 3.49e-31 | 111 |
| hsa0301020 | Cervix | CC | Ribosome | 85/1267 | 167/8465 | 3.17e-28 | 5.14e-26 | 3.04e-26 | 85 |
| hsa05171110 | Cervix | CC | Coronavirus disease - COVID-19 | 111/1267 | 232/8465 | 1.82e-33 | 5.90e-31 | 3.49e-31 | 111 |
| hsa03010110 | Cervix | CC | Ribosome | 85/1267 | 167/8465 | 3.17e-28 | 5.14e-26 | 3.04e-26 | 85 |
| hsa0301025 | Cervix | HSIL_HPV | Ribosome | 80/459 | 167/8465 | 9.61e-58 | 2.82e-55 | 2.28e-55 | 80 |
| hsa0517125 | Cervix | HSIL_HPV | Coronavirus disease - COVID-19 | 91/459 | 232/8465 | 2.14e-56 | 3.13e-54 | 2.53e-54 | 91 |
| hsa0301035 | Cervix | HSIL_HPV | Ribosome | 80/459 | 167/8465 | 9.61e-58 | 2.82e-55 | 2.28e-55 | 80 |
| hsa0517135 | Cervix | HSIL_HPV | Coronavirus disease - COVID-19 | 91/459 | 232/8465 | 2.14e-56 | 3.13e-54 | 2.53e-54 | 91 |
| Page: 1 2 3 4 5 6 7 |
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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 |
| RPS5 | SNV | Missense_Mutation | c.292N>A | p.Glu98Lys | p.E98K | P46782 | protein_coding | deleterious(0.02) | possibly_damaging(0.697) | TCGA-A2-A259-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| RPS5 | SNV | Missense_Mutation | c.58N>C | p.Phe20Leu | p.F20L | P46782 | protein_coding | deleterious(0.01) | possibly_damaging(0.691) | TCGA-A8-A0AD-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| RPS5 | SNV | Missense_Mutation | c.376N>G | p.Thr126Ala | p.T126A | P46782 | protein_coding | tolerated(0.1) | probably_damaging(0.977) | TCGA-BH-A0HA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| RPS5 | SNV | Missense_Mutation | c.7N>A | p.Glu3Lys | p.E3K | P46782 | protein_coding | deleterious(0.02) | benign(0.011) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RPS5 | SNV | Missense_Mutation | novel | c.212N>A | p.Arg71His | p.R71H | P46782 | protein_coding | deleterious(0.02) | probably_damaging(0.991) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| RPS5 | SNV | Missense_Mutation | c.351N>G | p.Ile117Met | p.I117M | P46782 | protein_coding | deleterious(0.05) | probably_damaging(0.951) | TCGA-JX-A3Q0-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD | |
| RPS5 | SNV | Missense_Mutation | rs768490326 | c.563A>G | p.Tyr188Cys | p.Y188C | P46782 | protein_coding | deleterious(0) | probably_damaging(0.99) | TCGA-AA-3663-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| RPS5 | SNV | Missense_Mutation | c.520N>T | p.Ala174Ser | p.A174S | P46782 | protein_coding | deleterious(0.03) | possibly_damaging(0.619) | TCGA-AA-3815-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RPS5 | SNV | Missense_Mutation | rs761762077 | c.179G>A | p.Arg60His | p.R60H | P46782 | protein_coding | deleterious(0.04) | probably_damaging(0.996) | TCGA-AA-A01P-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |
| RPS5 | SNV | Missense_Mutation | c.394N>A | p.Gly132Arg | p.G132R | P46782 | protein_coding | deleterious(0.04) | benign(0.414) | TCGA-AM-5821-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 |
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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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