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Gene: RPL39 |
Gene summary for RPL39 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RPL39 | Gene ID | 6170 |
| Gene name | ribosomal protein L39 | |
| Gene Alias | L39 | |
| Cytomap | Xq24 | |
| Gene Type | protein-coding | GO ID | GO:0002181 | UniProtAcc | P62891 |
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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 |
| 6170 | RPL39 | GSM4909281 | Human | Breast | IDC | 1.42e-06 | -1.37e-01 | 0.21 |
| 6170 | RPL39 | GSM4909282 | Human | Breast | IDC | 2.13e-25 | 2.72e-01 | -0.0288 |
| 6170 | RPL39 | GSM4909286 | Human | Breast | IDC | 5.89e-04 | 1.38e-01 | 0.1081 |
| 6170 | RPL39 | GSM4909293 | Human | Breast | IDC | 9.64e-07 | -7.53e-02 | 0.1581 |
| 6170 | RPL39 | GSM4909299 | Human | Breast | IDC | 2.07e-06 | 1.59e-01 | 0.035 |
| 6170 | RPL39 | GSM4909308 | Human | Breast | IDC | 1.28e-04 | -1.38e-01 | 0.158 |
| 6170 | RPL39 | GSM4909313 | Human | Breast | IDC | 3.74e-02 | -1.32e-01 | 0.0391 |
| 6170 | RPL39 | GSM4909317 | Human | Breast | IDC | 1.47e-04 | -1.76e-01 | 0.1355 |
| 6170 | RPL39 | GSM4909319 | Human | Breast | IDC | 6.98e-32 | -7.46e-01 | 0.1563 |
| 6170 | RPL39 | GSM4909320 | Human | Breast | IDC | 3.51e-03 | -2.62e-01 | 0.1575 |
| 6170 | RPL39 | GSM4909321 | Human | Breast | IDC | 2.43e-27 | -4.09e-01 | 0.1559 |
| 6170 | RPL39 | brca1 | Human | Breast | Precancer | 3.09e-94 | -1.05e+00 | -0.0338 |
| 6170 | RPL39 | brca2 | Human | Breast | Precancer | 2.96e-05 | -1.07e-01 | -0.024 |
| 6170 | RPL39 | M5 | Human | Breast | IDC | 7.16e-03 | -3.58e-01 | 0.1598 |
| 6170 | RPL39 | NCCBC14 | Human | Breast | DCIS | 2.56e-18 | -4.15e-01 | 0.2021 |
| 6170 | RPL39 | NCCBC5 | Human | Breast | DCIS | 1.44e-09 | -2.86e-01 | 0.2046 |
| 6170 | RPL39 | P1 | Human | Breast | IDC | 4.31e-10 | -2.96e-01 | 0.1527 |
| 6170 | RPL39 | P2 | Human | Breast | IDC | 4.76e-07 | -2.86e-01 | 0.21 |
| 6170 | RPL39 | DCIS2 | Human | Breast | DCIS | 2.17e-10 | -1.59e-01 | 0.0085 |
| 6170 | RPL39 | CA_HPV_2 | Human | Cervix | CC | 1.36e-24 | -3.15e-01 | 0.0391 |
| 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:000218112 | Liver | Cirrhotic | cytoplasmic translation | 120/4634 | 148/18723 | 2.95e-47 | 1.85e-43 | 120 |
| GO:000218122 | Liver | HCC | cytoplasmic translation | 132/7958 | 148/18723 | 9.09e-33 | 5.76e-30 | 132 |
| GO:000218132 | Liver | Cyst | cytoplasmic translation | 70/496 | 148/18723 | 9.01e-71 | 3.85e-67 | 70 |
| GO:00197306 | Liver | Cyst | antimicrobial humoral response | 11/496 | 122/18723 | 4.02e-04 | 1.24e-02 | 11 |
| GO:00021818 | Lung | IAC | cytoplasmic translation | 85/2061 | 148/18723 | 3.11e-43 | 1.85e-39 | 85 |
| GO:000218113 | Lung | AIS | cytoplasmic translation | 85/1849 | 148/18723 | 5.48e-47 | 3.19e-43 | 85 |
| GO:000218133 | Lung | MIAC | cytoplasmic translation | 73/967 | 148/18723 | 4.84e-54 | 2.48e-50 | 73 |
| GO:000218120 | Oral cavity | OSCC | cytoplasmic translation | 133/7305 | 148/18723 | 1.94e-38 | 2.46e-35 | 133 |
| GO:0002181110 | Oral cavity | LP | cytoplasmic translation | 124/4623 | 148/18723 | 5.09e-52 | 3.19e-48 | 124 |
| GO:000218126 | Oral cavity | EOLP | cytoplasmic translation | 102/2218 | 148/18723 | 7.91e-60 | 4.74e-56 | 102 |
| GO:000218134 | Oral cavity | NEOLP | cytoplasmic translation | 102/2005 | 148/18723 | 3.70e-64 | 2.20e-60 | 102 |
| GO:000218118 | Prostate | BPH | cytoplasmic translation | 115/3107 | 148/18723 | 1.08e-60 | 6.68e-57 | 115 |
| GO:000218119 | Prostate | Tumor | cytoplasmic translation | 115/3246 | 148/18723 | 1.36e-58 | 8.43e-55 | 115 |
| GO:000218128 | Skin | AK | cytoplasmic translation | 101/1910 | 148/18723 | 5.98e-65 | 3.54e-61 | 101 |
| GO:0002181112 | Skin | SCCIS | cytoplasmic translation | 58/919 | 148/18723 | 2.30e-37 | 1.22e-33 | 58 |
| GO:000218129 | Skin | cSCC | cytoplasmic translation | 127/4864 | 148/18723 | 4.83e-53 | 7.57e-50 | 127 |
| GO:00021816 | Stomach | GC | cytoplasmic translation | 62/1159 | 148/18723 | 5.06e-36 | 2.75e-32 | 62 |
| GO:0019730 | Stomach | GC | antimicrobial humoral response | 25/1159 | 122/18723 | 9.62e-08 | 6.08e-06 | 25 |
| GO:0006959 | Stomach | GC | humoral immune response | 42/1159 | 317/18723 | 2.59e-06 | 1.10e-04 | 42 |
| GO:0019731 | Stomach | GC | antibacterial humoral response | 13/1159 | 60/18723 | 6.18e-05 | 1.40e-03 | 13 |
| Page: 1 2 3 4 5 |
| 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 |
| RPL39 | SNV | Missense_Mutation | c.61N>T | p.Arg21Cys | p.R21C | P62891 | protein_coding | tolerated(0.24) | benign(0.007) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| RPL39 | SNV | Missense_Mutation | c.79A>G | p.Ile27Val | p.I27V | P62891 | protein_coding | tolerated(0.18) | benign(0.047) | TCGA-G4-6588-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| RPL39 | SNV | Missense_Mutation | c.46N>G | p.Lys16Glu | p.K16E | P62891 | protein_coding | deleterious(0.02) | probably_damaging(0.936) | TCGA-AX-A062-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| RPL39 | SNV | Missense_Mutation | c.61N>T | p.Arg21Cys | p.R21C | P62891 | protein_coding | tolerated(0.24) | benign(0.007) | TCGA-B5-A0JY-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD | |
| RPL39 | SNV | Missense_Mutation | c.61N>T | p.Arg21Cys | p.R21C | P62891 | protein_coding | tolerated(0.24) | benign(0.007) | TCGA-BS-A0TC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RPL39 | SNV | Missense_Mutation | c.129N>A | p.His43Gln | p.H43Q | P62891 | protein_coding | deleterious(0.04) | possibly_damaging(0.776) | TCGA-BS-A0UJ-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 |
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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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