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Gene: RPL4 |
Gene summary for RPL4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RPL4 | Gene ID | 6124 |
| Gene name | ribosomal protein L4 | |
| Gene Alias | L4 | |
| Cytomap | 15q22.31 | |
| Gene Type | protein-coding | GO ID | GO:0002181 | UniProtAcc | P36578 |
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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 |
| 6124 | RPL4 | GSM4909280 | Human | Breast | Precancer | 2.69e-05 | -5.59e-01 | 0.0305 |
| 6124 | RPL4 | GSM4909281 | Human | Breast | IDC | 2.15e-10 | -2.21e-01 | 0.21 |
| 6124 | RPL4 | GSM4909282 | Human | Breast | IDC | 3.63e-03 | 1.41e-01 | -0.0288 |
| 6124 | RPL4 | GSM4909287 | Human | Breast | IDC | 3.36e-05 | -2.60e-01 | 0.2057 |
| 6124 | RPL4 | GSM4909288 | Human | Breast | IDC | 2.32e-02 | -2.63e-01 | 0.0988 |
| 6124 | RPL4 | GSM4909292 | Human | Breast | IDC | 4.74e-06 | -6.36e-01 | 0.1236 |
| 6124 | RPL4 | GSM4909293 | Human | Breast | IDC | 3.69e-46 | -3.99e-01 | 0.1581 |
| 6124 | RPL4 | GSM4909294 | Human | Breast | IDC | 9.14e-22 | -5.35e-01 | 0.2022 |
| 6124 | RPL4 | GSM4909296 | Human | Breast | IDC | 6.39e-03 | -1.20e-02 | 0.1524 |
| 6124 | RPL4 | GSM4909297 | Human | Breast | IDC | 3.60e-20 | -2.08e-01 | 0.1517 |
| 6124 | RPL4 | GSM4909298 | Human | Breast | IDC | 7.29e-13 | -1.87e-01 | 0.1551 |
| 6124 | RPL4 | GSM4909301 | Human | Breast | IDC | 7.95e-45 | -5.91e-01 | 0.1577 |
| 6124 | RPL4 | GSM4909302 | Human | Breast | IDC | 9.75e-18 | -4.39e-01 | 0.1545 |
| 6124 | RPL4 | GSM4909303 | Human | Breast | IDC | 2.37e-03 | -3.00e-01 | 0.0438 |
| 6124 | RPL4 | GSM4909304 | Human | Breast | IDC | 2.12e-03 | -8.72e-02 | 0.1636 |
| 6124 | RPL4 | GSM4909305 | Human | Breast | IDC | 4.22e-04 | 1.58e-01 | 0.0436 |
| 6124 | RPL4 | GSM4909306 | Human | Breast | IDC | 8.62e-13 | -2.30e-01 | 0.1564 |
| 6124 | RPL4 | GSM4909307 | Human | Breast | IDC | 2.14e-07 | -2.42e-01 | 0.1569 |
| 6124 | RPL4 | GSM4909309 | Human | Breast | IDC | 8.68e-10 | -3.36e-01 | 0.0483 |
| 6124 | RPL4 | GSM4909311 | Human | Breast | IDC | 4.18e-36 | -3.48e-01 | 0.1534 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 |
| 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:000218114 | Breast | IDC | cytoplasmic translation | 82/1434 | 148/18723 | 2.60e-52 | 1.48e-48 | 82 |
| GO:00325432 | Breast | IDC | mitochondrial translation | 13/1434 | 76/18723 | 4.81e-03 | 3.67e-02 | 13 |
| GO:000218124 | Breast | DCIS | cytoplasmic translation | 82/1390 | 148/18723 | 2.21e-53 | 1.25e-49 | 82 |
| GO:003254311 | Breast | DCIS | mitochondrial translation | 13/1390 | 76/18723 | 3.70e-03 | 2.99e-02 | 13 |
| 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:00021811 | Colorectum | SER | cytoplasmic translation | 102/2897 | 148/18723 | 1.38e-48 | 8.49e-45 | 102 |
| GO:00021812 | Colorectum | MSS | cytoplasmic translation | 108/3467 | 148/18723 | 1.78e-47 | 1.11e-43 | 108 |
| GO:00021813 | Colorectum | MSI-H | cytoplasmic translation | 100/1319 | 148/18723 | 1.50e-79 | 8.31e-76 | 100 |
| GO:00021814 | Colorectum | FAP | cytoplasmic translation | 76/2622 | 148/18723 | 3.31e-27 | 2.03e-23 | 76 |
| GO:00021815 | Colorectum | CRC | cytoplasmic translation | 70/2078 | 148/18723 | 1.53e-28 | 9.16e-25 | 70 |
| 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:00325435 | Esophagus | HGIN | mitochondrial translation | 23/2587 | 76/18723 | 1.61e-04 | 3.16e-03 | 23 |
| GO:01400534 | Esophagus | HGIN | mitochondrial gene expression | 27/2587 | 108/18723 | 1.34e-03 | 1.57e-02 | 27 |
| GO:0016072110 | Esophagus | ESCC | rRNA metabolic process | 197/8552 | 236/18723 | 1.31e-33 | 1.18e-30 | 197 |
| GO:0002181111 | Esophagus | ESCC | cytoplasmic translation | 135/8552 | 148/18723 | 4.17e-32 | 2.65e-29 | 135 |
| Page: 1 2 3 4 5 6 7 |
| 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 |
| RPL4 | SNV | Missense_Mutation | c.535N>C | p.Asp179His | p.D179H | P36578 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-B6-A0RE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| RPL4 | SNV | Missense_Mutation | novel | c.98G>A | p.Arg33Gln | p.R33Q | P36578 | protein_coding | deleterious(0.01) | probably_damaging(0.918) | TCGA-GM-A2DK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | CR |
| RPL4 | SNV | Missense_Mutation | c.567N>C | p.Met189Ile | p.M189I | P36578 | protein_coding | tolerated(0.85) | benign(0.017) | TCGA-EK-A3GM-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RPL4 | SNV | Missense_Mutation | rs768431706 | c.181N>G | p.Gln61Glu | p.Q61E | P36578 | protein_coding | deleterious(0.04) | possibly_damaging(0.491) | TCGA-IR-A3LA-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| RPL4 | SNV | Missense_Mutation | c.966N>C | p.Leu322Phe | p.L322F | P36578 | protein_coding | tolerated(0.46) | benign(0.02) | TCGA-IR-A3LK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD | |
| RPL4 | SNV | Missense_Mutation | novel | c.260C>T | p.Ser87Phe | p.S87F | P36578 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-MY-A5BF-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | CR |
| RPL4 | SNV | Missense_Mutation | rs780532132 | c.37N>A | p.Glu13Lys | p.E13K | P36578 | protein_coding | tolerated(0.48) | possibly_damaging(0.449) | TCGA-AA-3715-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| RPL4 | SNV | Missense_Mutation | rs752263296 | c.289N>T | p.Arg97Cys | p.R97C | P36578 | protein_coding | deleterious(0.02) | possibly_damaging(0.458) | TCGA-AA-3956-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| RPL4 | SNV | Missense_Mutation | novel | c.1106N>T | p.Ala369Val | p.A369V | P36578 | protein_coding | tolerated(0.35) | benign(0) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RPL4 | SNV | Missense_Mutation | novel | c.563N>A | p.Arg188Gln | p.R188Q | P36578 | protein_coding | tolerated(0.13) | benign(0.166) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 |
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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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