|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: RPL6 |
Gene summary for RPL6 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RPL6 | Gene ID | 6128 |
| Gene name | ribosomal protein L6 | |
| Gene Alias | L6 | |
| Cytomap | 12q24.13 | |
| Gene Type | protein-coding | GO ID | GO:0000027 | UniProtAcc | A0A024RBK3 |
Top |
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 |
| 6128 | RPL6 | GSM4909281 | Human | Breast | IDC | 5.14e-36 | -2.99e-01 | 0.21 |
| 6128 | RPL6 | GSM4909282 | Human | Breast | IDC | 1.95e-88 | -5.08e-01 | -0.0288 |
| 6128 | RPL6 | GSM4909286 | Human | Breast | IDC | 5.69e-32 | 2.03e-01 | 0.1081 |
| 6128 | RPL6 | GSM4909287 | Human | Breast | IDC | 1.09e-52 | -5.59e-01 | 0.2057 |
| 6128 | RPL6 | GSM4909290 | Human | Breast | IDC | 1.26e-11 | -1.93e-01 | 0.2096 |
| 6128 | RPL6 | GSM4909291 | Human | Breast | IDC | 5.30e-28 | -3.48e-01 | 0.1753 |
| 6128 | RPL6 | GSM4909293 | Human | Breast | IDC | 1.14e-10 | -8.84e-02 | 0.1581 |
| 6128 | RPL6 | GSM4909295 | Human | Breast | IDC | 1.25e-15 | -3.91e-01 | 0.0898 |
| 6128 | RPL6 | GSM4909297 | Human | Breast | IDC | 1.37e-06 | -1.83e-01 | 0.1517 |
| 6128 | RPL6 | GSM4909301 | Human | Breast | IDC | 1.00e-51 | -3.78e-01 | 0.1577 |
| 6128 | RPL6 | GSM4909302 | Human | Breast | IDC | 3.13e-16 | -2.72e-01 | 0.1545 |
| 6128 | RPL6 | GSM4909304 | Human | Breast | IDC | 1.96e-24 | -1.87e-01 | 0.1636 |
| 6128 | RPL6 | GSM4909307 | Human | Breast | IDC | 1.38e-07 | -1.38e-01 | 0.1569 |
| 6128 | RPL6 | GSM4909308 | Human | Breast | IDC | 1.49e-11 | -1.53e-01 | 0.158 |
| 6128 | RPL6 | GSM4909309 | Human | Breast | IDC | 2.27e-04 | -1.85e-01 | 0.0483 |
| 6128 | RPL6 | GSM4909311 | Human | Breast | IDC | 3.04e-18 | -3.68e-01 | 0.1534 |
| 6128 | RPL6 | GSM4909312 | Human | Breast | IDC | 8.51e-03 | -1.22e-01 | 0.1552 |
| 6128 | RPL6 | GSM4909313 | Human | Breast | IDC | 1.27e-11 | -2.79e-01 | 0.0391 |
| 6128 | RPL6 | GSM4909315 | Human | Breast | IDC | 7.17e-18 | -2.42e-01 | 0.21 |
| 6128 | RPL6 | GSM4909316 | Human | Breast | IDC | 7.04e-17 | -5.17e-01 | 0.21 |
| 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. |
Top |
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: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:00000279 | Breast | Precancer | ribosomal large subunit assembly | 9/1080 | 27/18723 | 1.24e-05 | 3.19e-04 | 9 |
| 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:004225514 | Breast | IDC | ribosome assembly | 21/1434 | 61/18723 | 1.98e-09 | 1.76e-07 | 21 |
| GO:004227314 | Breast | IDC | ribosomal large subunit biogenesis | 22/1434 | 72/18723 | 1.04e-08 | 7.67e-07 | 22 |
| GO:004225414 | Breast | IDC | ribosome biogenesis | 52/1434 | 299/18723 | 1.90e-08 | 1.32e-06 | 52 |
| GO:000002714 | Breast | IDC | ribosomal large subunit assembly | 9/1434 | 27/18723 | 1.17e-04 | 2.17e-03 | 9 |
| 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 |
| GO:007182624 | Breast | DCIS | ribonucleoprotein complex subunit organization | 52/1390 | 227/18723 | 1.54e-13 | 3.95e-11 | 52 |
| GO:002261824 | Breast | DCIS | ribonucleoprotein complex assembly | 51/1390 | 220/18723 | 1.60e-13 | 3.95e-11 | 51 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0517164 | Oral cavity | NEOLP | Coronavirus disease - COVID-19 | 112/1112 | 232/8465 | 8.85e-40 | 2.82e-37 | 1.77e-37 | 112 |
| hsa0301064 | Oral cavity | NEOLP | Ribosome | 81/1112 | 167/8465 | 4.35e-29 | 6.91e-27 | 4.35e-27 | 81 |
| hsa0517174 | Oral cavity | NEOLP | Coronavirus disease - COVID-19 | 112/1112 | 232/8465 | 8.85e-40 | 2.82e-37 | 1.77e-37 | 112 |
| hsa0301074 | Oral cavity | NEOLP | Ribosome | 81/1112 | 167/8465 | 4.35e-29 | 6.91e-27 | 4.35e-27 | 81 |
| hsa0301028 | Prostate | BPH | Ribosome | 104/1718 | 167/8465 | 8.04e-33 | 1.33e-30 | 8.21e-31 | 104 |
| hsa0517128 | Prostate | BPH | Coronavirus disease - COVID-19 | 115/1718 | 232/8465 | 5.65e-24 | 2.07e-22 | 1.28e-22 | 115 |
| hsa03010113 | Prostate | BPH | Ribosome | 104/1718 | 167/8465 | 8.04e-33 | 1.33e-30 | 8.21e-31 | 104 |
| hsa05171113 | Prostate | BPH | Coronavirus disease - COVID-19 | 115/1718 | 232/8465 | 5.65e-24 | 2.07e-22 | 1.28e-22 | 115 |
| hsa0301029 | Prostate | Tumor | Ribosome | 104/1791 | 167/8465 | 3.53e-31 | 5.84e-29 | 3.62e-29 | 104 |
| hsa0517129 | Prostate | Tumor | Coronavirus disease - COVID-19 | 118/1791 | 232/8465 | 3.58e-24 | 1.69e-22 | 1.05e-22 | 118 |
| hsa0301037 | Prostate | Tumor | Ribosome | 104/1791 | 167/8465 | 3.53e-31 | 5.84e-29 | 3.62e-29 | 104 |
| hsa0517137 | Prostate | Tumor | Coronavirus disease - COVID-19 | 118/1791 | 232/8465 | 3.58e-24 | 1.69e-22 | 1.05e-22 | 118 |
| hsa0301012 | Stomach | GC | Ribosome | 64/708 | 167/8465 | 2.58e-27 | 8.26e-25 | 5.81e-25 | 64 |
| hsa0517112 | Stomach | GC | Coronavirus disease - COVID-19 | 71/708 | 232/8465 | 2.32e-23 | 3.72e-21 | 2.62e-21 | 71 |
| hsa0301013 | Stomach | GC | Ribosome | 64/708 | 167/8465 | 2.58e-27 | 8.26e-25 | 5.81e-25 | 64 |
| hsa0517113 | Stomach | GC | Coronavirus disease - COVID-19 | 71/708 | 232/8465 | 2.32e-23 | 3.72e-21 | 2.62e-21 | 71 |
| hsa0301021 | Stomach | CAG with IM | Ribosome | 63/640 | 167/8465 | 5.86e-29 | 1.86e-26 | 1.31e-26 | 63 |
| hsa0517121 | Stomach | CAG with IM | Coronavirus disease - COVID-19 | 68/640 | 232/8465 | 9.36e-24 | 1.49e-21 | 1.04e-21 | 68 |
| hsa0301031 | Stomach | CAG with IM | Ribosome | 63/640 | 167/8465 | 5.86e-29 | 1.86e-26 | 1.31e-26 | 63 |
| hsa0517131 | Stomach | CAG with IM | Coronavirus disease - COVID-19 | 68/640 | 232/8465 | 9.36e-24 | 1.49e-21 | 1.04e-21 | 68 |
| Page: 1 2 3 4 5 6 7 |
Top |
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 |
Top |
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 |
Top |
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 |
| RPL6 | SNV | Missense_Mutation | novel | c.28G>C | p.Asp10His | p.D10H | Q02878 | protein_coding | tolerated(0.05) | benign(0.159) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
| RPL6 | SNV | Missense_Mutation | novel | c.521N>G | p.Leu174Arg | p.L174R | Q02878 | protein_coding | deleterious(0) | probably_damaging(0.972) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| RPL6 | SNV | Missense_Mutation | c.241N>A | p.Glu81Lys | p.E81K | Q02878 | protein_coding | tolerated(0.11) | probably_damaging(0.996) | TCGA-DS-A0VM-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD | |
| RPL6 | SNV | Missense_Mutation | rs747383826 | c.467G>A | p.Arg156His | p.R156H | Q02878 | protein_coding | tolerated(0.2) | benign(0.021) | TCGA-EA-A3HU-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| RPL6 | SNV | Missense_Mutation | c.578N>G | p.Phe193Cys | p.F193C | Q02878 | protein_coding | deleterious(0.02) | benign(0.078) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| RPL6 | SNV | Missense_Mutation | c.394C>A | p.Pro132Thr | p.P132T | Q02878 | protein_coding | tolerated(0.16) | benign(0.04) | TCGA-AA-A02R-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| RPL6 | SNV | Missense_Mutation | c.616G>A | p.Val206Ile | p.V206I | Q02878 | protein_coding | deleterious(0.05) | benign(0.344) | TCGA-CM-6674-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| RPL6 | SNV | Missense_Mutation | c.578N>G | p.Phe193Cys | p.F193C | Q02878 | protein_coding | deleterious(0.02) | benign(0.078) | TCGA-AG-3892-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| RPL6 | SNV | Missense_Mutation | c.638N>T | p.Thr213Ile | p.T213I | Q02878 | protein_coding | tolerated(0.05) | possibly_damaging(0.566) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| RPL6 | SNV | Missense_Mutation | novel | c.149T>G | p.Leu50Arg | p.L50R | Q02878 | protein_coding | deleterious(0.01) | possibly_damaging(0.848) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 |
Top |
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 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |