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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 | CA_HPV_3 | Human | Cervix | CC | 1.18e-16 | -1.23e-01 | 0.0414 |
| 6170 | RPL39 | HSIL_HPV_2 | Human | Cervix | HSIL_HPV | 4.27e-03 | 1.10e-01 | 0.0208 |
| 6170 | RPL39 | N_HPV_1 | Human | Cervix | N_HPV | 1.17e-02 | 7.00e-02 | 0.0079 |
| 6170 | RPL39 | CCI_1 | Human | Cervix | CC | 2.56e-59 | -2.12e+00 | 0.528 |
| 6170 | RPL39 | CCI_2 | Human | Cervix | CC | 2.63e-63 | -2.02e+00 | 0.5249 |
| 6170 | RPL39 | CCI_3 | Human | Cervix | CC | 4.17e-72 | -2.13e+00 | 0.516 |
| 6170 | RPL39 | CCII_1 | Human | Cervix | CC | 1.48e-90 | -2.14e+00 | 0.3249 |
| 6170 | RPL39 | Tumor | Human | Cervix | CC | 3.47e-32 | 2.09e-01 | 0.1241 |
| 6170 | RPL39 | sample1 | Human | Cervix | CC | 5.22e-12 | -2.78e-01 | 0.0959 |
| 6170 | RPL39 | sample3 | Human | Cervix | CC | 2.19e-10 | 1.40e-01 | 0.1387 |
| 6170 | RPL39 | H2 | Human | Cervix | HSIL_HPV | 3.72e-77 | -5.54e-01 | 0.0632 |
| 6170 | RPL39 | T1 | Human | Cervix | CC | 8.69e-43 | -4.35e-01 | 0.0918 |
| 6170 | RPL39 | T3 | Human | Cervix | CC | 9.30e-11 | 1.53e-01 | 0.1389 |
| 6170 | RPL39 | HTA11_3410_2000001011 | Human | Colorectum | AD | 8.74e-05 | 1.95e-01 | 0.0155 |
| 6170 | RPL39 | HTA11_2487_2000001011 | Human | Colorectum | SER | 4.93e-17 | 7.84e-01 | -0.1808 |
| 6170 | RPL39 | HTA11_2951_2000001011 | Human | Colorectum | AD | 1.91e-13 | 9.55e-01 | 0.0216 |
| 6170 | RPL39 | HTA11_1938_2000001011 | Human | Colorectum | AD | 7.60e-13 | 6.47e-01 | -0.0811 |
| 6170 | RPL39 | HTA11_78_2000001011 | Human | Colorectum | AD | 5.81e-27 | 8.85e-01 | -0.1088 |
| 6170 | RPL39 | HTA11_347_2000001011 | Human | Colorectum | AD | 6.41e-24 | 6.85e-01 | -0.1954 |
| 6170 | RPL39 | HTA11_411_2000001011 | Human | Colorectum | SER | 2.99e-05 | 8.51e-01 | -0.2602 |
| 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:00197307 | Breast | Precancer | antimicrobial humoral response | 19/1080 | 122/18723 | 7.02e-05 | 1.40e-03 | 19 |
| GO:00618446 | Breast | Precancer | antimicrobial humoral immune response mediated by antimicrobial peptide | 14/1080 | 79/18723 | 1.53e-04 | 2.61e-03 | 14 |
| GO:000218114 | Breast | IDC | cytoplasmic translation | 82/1434 | 148/18723 | 2.60e-52 | 1.48e-48 | 82 |
| GO:001973011 | Breast | IDC | antimicrobial humoral response | 23/1434 | 122/18723 | 4.67e-05 | 1.04e-03 | 23 |
| GO:006184411 | Breast | IDC | antimicrobial humoral immune response mediated by antimicrobial peptide | 16/1434 | 79/18723 | 2.75e-04 | 4.24e-03 | 16 |
| GO:00069596 | Breast | IDC | humoral immune response | 40/1434 | 317/18723 | 1.25e-03 | 1.33e-02 | 40 |
| GO:000218124 | Breast | DCIS | cytoplasmic translation | 82/1390 | 148/18723 | 2.21e-53 | 1.25e-49 | 82 |
| GO:001973021 | Breast | DCIS | antimicrobial humoral response | 21/1390 | 122/18723 | 2.40e-04 | 3.75e-03 | 21 |
| GO:006184421 | Breast | DCIS | antimicrobial humoral immune response mediated by antimicrobial peptide | 15/1390 | 79/18723 | 6.25e-04 | 7.87e-03 | 15 |
| GO:000695911 | Breast | DCIS | humoral immune response | 37/1390 | 317/18723 | 4.16e-03 | 3.29e-02 | 37 |
| GO:000218110 | Cervix | CC | cytoplasmic translation | 96/2311 | 148/18723 | 4.87e-51 | 2.91e-47 | 96 |
| GO:00197308 | Cervix | CC | antimicrobial humoral response | 27/2311 | 122/18723 | 1.70e-03 | 1.29e-02 | 27 |
| GO:00618447 | Cervix | CC | antimicrobial humoral immune response mediated by antimicrobial peptide | 18/2311 | 79/18723 | 6.82e-03 | 3.74e-02 | 18 |
| GO:00069597 | Cervix | CC | humoral immune response | 54/2311 | 317/18723 | 8.57e-03 | 4.42e-02 | 54 |
| GO:000218115 | Cervix | HSIL_HPV | cytoplasmic translation | 86/737 | 148/18723 | 3.97e-82 | 1.91e-78 | 86 |
| GO:000695912 | Cervix | HSIL_HPV | humoral immune response | 39/737 | 317/18723 | 2.88e-10 | 7.02e-08 | 39 |
| GO:001973012 | Cervix | HSIL_HPV | antimicrobial humoral response | 18/737 | 122/18723 | 1.35e-06 | 6.21e-05 | 18 |
| GO:00427423 | Cervix | HSIL_HPV | defense response to bacterium | 30/737 | 350/18723 | 5.82e-05 | 1.40e-03 | 30 |
| GO:006184412 | Cervix | HSIL_HPV | antimicrobial humoral immune response mediated by antimicrobial peptide | 11/737 | 79/18723 | 2.57e-04 | 4.44e-03 | 11 |
| 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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