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Gene: RPL5 |
Gene summary for RPL5 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RPL5 | Gene ID | 6125 |
| Gene name | ribosomal protein L5 | |
| Gene Alias | L5 | |
| Cytomap | 1p22.1 | |
| Gene Type | protein-coding | GO ID | GO:0000027 | UniProtAcc | A2RUM7 |
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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 |
| 6125 | RPL5 | GSM4909281 | Human | Breast | IDC | 2.04e-43 | -4.12e-01 | 0.21 |
| 6125 | RPL5 | GSM4909285 | Human | Breast | IDC | 9.31e-19 | 1.96e-01 | 0.21 |
| 6125 | RPL5 | GSM4909287 | Human | Breast | IDC | 1.26e-06 | -2.31e-01 | 0.2057 |
| 6125 | RPL5 | GSM4909290 | Human | Breast | IDC | 7.19e-24 | -3.74e-01 | 0.2096 |
| 6125 | RPL5 | GSM4909293 | Human | Breast | IDC | 7.57e-29 | -2.25e-01 | 0.1581 |
| 6125 | RPL5 | GSM4909294 | Human | Breast | IDC | 4.95e-03 | -1.37e-01 | 0.2022 |
| 6125 | RPL5 | GSM4909297 | Human | Breast | IDC | 8.26e-13 | -2.14e-01 | 0.1517 |
| 6125 | RPL5 | GSM4909298 | Human | Breast | IDC | 1.10e-19 | -1.75e-01 | 0.1551 |
| 6125 | RPL5 | GSM4909301 | Human | Breast | IDC | 9.59e-91 | -8.02e-01 | 0.1577 |
| 6125 | RPL5 | GSM4909302 | Human | Breast | IDC | 2.35e-18 | -3.50e-01 | 0.1545 |
| 6125 | RPL5 | GSM4909306 | Human | Breast | IDC | 5.43e-18 | -1.97e-01 | 0.1564 |
| 6125 | RPL5 | GSM4909307 | Human | Breast | IDC | 1.32e-28 | -3.66e-01 | 0.1569 |
| 6125 | RPL5 | GSM4909308 | Human | Breast | IDC | 1.28e-41 | -3.97e-01 | 0.158 |
| 6125 | RPL5 | GSM4909309 | Human | Breast | IDC | 1.38e-05 | -2.34e-01 | 0.0483 |
| 6125 | RPL5 | GSM4909311 | Human | Breast | IDC | 8.32e-16 | -1.92e-01 | 0.1534 |
| 6125 | RPL5 | GSM4909313 | Human | Breast | IDC | 1.12e-07 | -2.62e-01 | 0.0391 |
| 6125 | RPL5 | GSM4909315 | Human | Breast | IDC | 3.42e-03 | -1.30e-01 | 0.21 |
| 6125 | RPL5 | GSM4909316 | Human | Breast | IDC | 2.54e-02 | -2.70e-01 | 0.21 |
| 6125 | RPL5 | GSM4909317 | Human | Breast | IDC | 4.71e-16 | -2.58e-01 | 0.1355 |
| 6125 | RPL5 | GSM4909318 | Human | Breast | IDC | 1.55e-04 | -4.28e-01 | 0.2031 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 |
| 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:00064179 | Breast | Precancer | regulation of translation | 67/1080 | 468/18723 | 4.71e-12 | 7.64e-10 | 67 |
| GO:00457279 | Breast | Precancer | positive regulation of translation | 32/1080 | 136/18723 | 5.89e-12 | 9.27e-10 | 32 |
| GO:00422559 | Breast | Precancer | ribosome assembly | 21/1080 | 61/18723 | 1.06e-11 | 1.53e-09 | 21 |
| GO:00422739 | Breast | Precancer | ribosomal large subunit biogenesis | 22/1080 | 72/18723 | 5.03e-11 | 5.61e-09 | 22 |
| GO:00342509 | Breast | Precancer | positive regulation of cellular amide metabolic process | 33/1080 | 162/18723 | 1.72e-10 | 1.77e-08 | 33 |
| GO:00458619 | Breast | Precancer | negative regulation of proteolysis | 50/1080 | 351/18723 | 2.99e-09 | 2.39e-07 | 50 |
| GO:19033209 | Breast | Precancer | regulation of protein modification by small protein conjugation or removal | 38/1080 | 242/18723 | 1.71e-08 | 1.17e-06 | 38 |
| GO:00063646 | Breast | Precancer | rRNA processing | 35/1080 | 225/18723 | 7.90e-08 | 4.60e-06 | 35 |
| GO:19033219 | Breast | Precancer | negative regulation of protein modification by small protein conjugation or removal | 21/1080 | 95/18723 | 8.09e-08 | 4.61e-06 | 21 |
| GO:00160726 | Breast | Precancer | rRNA metabolic process | 36/1080 | 236/18723 | 8.59e-08 | 4.84e-06 | 36 |
| GO:00313969 | Breast | Precancer | regulation of protein ubiquitination | 33/1080 | 210/18723 | 1.45e-07 | 7.82e-06 | 33 |
| GO:00313979 | Breast | Precancer | negative regulation of protein ubiquitination | 19/1080 | 83/18723 | 1.85e-07 | 9.54e-06 | 19 |
| GO:19033629 | Breast | Precancer | regulation of cellular protein catabolic process | 36/1080 | 255/18723 | 6.03e-07 | 2.55e-05 | 36 |
| GO:19017969 | Breast | Precancer | regulation of signal transduction by p53 class mediator | 19/1080 | 93/18723 | 1.20e-06 | 4.60e-05 | 19 |
| GO:00421769 | Breast | Precancer | regulation of protein catabolic process | 47/1080 | 391/18723 | 1.50e-06 | 5.58e-05 | 47 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 |
| 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 |
| RPL5 | SNV | Missense_Mutation | rs764649729 | c.160N>T | p.Arg54Cys | p.R54C | P46777 | protein_coding | tolerated(0.09) | benign(0.315) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
| RPL5 | SNV | Missense_Mutation | c.290C>G | p.Ala97Gly | p.A97G | P46777 | protein_coding | deleterious(0.01) | possibly_damaging(0.657) | TCGA-A7-A0D9-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | SD | |
| RPL5 | deletion | Frame_Shift_Del | c.177_183delNNNNNNN | p.Ile60ValfsTer8 | p.I60Vfs*8 | P46777 | protein_coding | TCGA-BH-A0DE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |||
| RPL5 | SNV | Missense_Mutation | rs775560628 | c.626N>A | p.Arg209His | p.R209H | P46777 | protein_coding | tolerated(0.31) | benign(0.001) | TCGA-EA-A410-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| RPL5 | SNV | Missense_Mutation | novel | c.235N>C | p.Tyr79His | p.Y79H | P46777 | protein_coding | tolerated(0.07) | benign(0.111) | TCGA-A6-2672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| RPL5 | SNV | Missense_Mutation | rs200315052 | c.877N>T | p.Arg293Trp | p.R293W | P46777 | protein_coding | tolerated(0.14) | benign(0) | TCGA-A6-5657-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Ancillary | leucovorin | SD |
| RPL5 | SNV | Missense_Mutation | c.374N>C | p.Val125Ala | p.V125A | P46777 | protein_coding | tolerated(0.37) | benign(0.026) | TCGA-AA-3663-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| RPL5 | SNV | Missense_Mutation | rs746120360 | c.619N>C | p.Tyr207His | p.Y207H | P46777 | protein_coding | deleterious(0.04) | benign(0.35) | TCGA-AU-6004-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RPL5 | SNV | Missense_Mutation | c.374T>C | p.Val125Ala | p.V125A | P46777 | protein_coding | tolerated(0.37) | benign(0.026) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| RPL5 | SNV | Missense_Mutation | c.244N>A | p.Glu82Lys | p.E82K | P46777 | protein_coding | tolerated(0.05) | benign(0.179) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| Page: 1 2 3 4 5 |
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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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