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Gene: RPS16 |
Gene summary for RPS16 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RPS16 | Gene ID | 6217 |
| Gene name | ribosomal protein S16 | |
| Gene Alias | S16 | |
| Cytomap | 19q13.2 | |
| Gene Type | protein-coding | GO ID | GO:0000462 | UniProtAcc | P62249 |
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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 |
| 6217 | RPS16 | AEH-subject5 | Human | Endometrium | AEH | 3.98e-36 | -5.94e-01 | -0.2953 |
| 6217 | RPS16 | EEC-subject1 | Human | Endometrium | EEC | 6.45e-37 | -5.08e-01 | -0.2682 |
| 6217 | RPS16 | EEC-subject2 | Human | Endometrium | EEC | 4.40e-21 | -3.63e-01 | -0.2607 |
| 6217 | RPS16 | EEC-subject3 | Human | Endometrium | EEC | 5.03e-10 | -3.25e-01 | -0.2525 |
| 6217 | RPS16 | EEC-subject4 | Human | Endometrium | EEC | 8.08e-46 | -5.75e-01 | -0.2571 |
| 6217 | RPS16 | EEC-subject5 | Human | Endometrium | EEC | 8.10e-46 | -5.69e-01 | -0.249 |
| 6217 | RPS16 | GSM5276935 | Human | Endometrium | EEC | 5.92e-14 | -1.72e-01 | -0.123 |
| 6217 | RPS16 | GSM6177620_NYU_UCEC1_lib2_lib2 | Human | Endometrium | EEC | 5.77e-03 | -1.87e-01 | -0.1875 |
| 6217 | RPS16 | GSM6177620_NYU_UCEC1_lib3_lib3 | Human | Endometrium | EEC | 2.96e-03 | -1.76e-01 | -0.1883 |
| 6217 | RPS16 | GSM6177621_NYU_UCEC2_lib1_lib1 | Human | Endometrium | EEC | 1.43e-04 | -1.60e-01 | -0.1934 |
| 6217 | RPS16 | GSM6177622_NYU_UCEC3_lib1_lib1 | Human | Endometrium | EEC | 2.04e-07 | -2.42e-01 | -0.1917 |
| 6217 | RPS16 | GSM6177622_NYU_UCEC3_lib2_lib2 | Human | Endometrium | EEC | 1.22e-09 | -3.09e-01 | -0.1916 |
| 6217 | RPS16 | GSM6177623_NYU_UCEC3_Vis | Human | Endometrium | EEC | 1.95e-29 | -3.46e-01 | -0.1269 |
| 6217 | RPS16 | LZE11D | Human | Esophagus | HGIN | 5.95e-10 | -5.80e-01 | -0.005 |
| 6217 | RPS16 | LZE2D | Human | Esophagus | HGIN | 2.06e-19 | 2.05e+00 | 0.0642 |
| 6217 | RPS16 | LZE2T | Human | Esophagus | ESCC | 2.31e-23 | 2.11e+00 | 0.082 |
| 6217 | RPS16 | LZE3D | Human | Esophagus | HGIN | 2.95e-19 | 2.17e+00 | 0.0668 |
| 6217 | RPS16 | LZE4T | Human | Esophagus | ESCC | 8.32e-46 | 2.14e+00 | 0.0811 |
| 6217 | RPS16 | LZE5T | Human | Esophagus | ESCC | 1.23e-18 | 2.51e+00 | 0.0514 |
| 6217 | RPS16 | LZE7T | Human | Esophagus | ESCC | 4.14e-26 | 2.99e+00 | 0.0667 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 |
| 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 | ||
| 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:00422549 | Breast | Precancer | ribosome biogenesis | 52/1080 | 299/18723 | 7.35e-13 | 1.51e-10 | 52 |
| GO:00422749 | Breast | Precancer | ribosomal small subunit biogenesis | 21/1080 | 73/18723 | 4.84e-10 | 4.39e-08 | 21 |
| GO:00063646 | Breast | Precancer | rRNA processing | 35/1080 | 225/18723 | 7.90e-08 | 4.60e-06 | 35 |
| GO:00160726 | Breast | Precancer | rRNA metabolic process | 36/1080 | 236/18723 | 8.59e-08 | 4.84e-06 | 36 |
| GO:00487329 | Breast | Precancer | gland development | 49/1080 | 436/18723 | 6.11e-06 | 1.73e-04 | 49 |
| GO:00974216 | Breast | Precancer | liver regeneration | 10/1080 | 35/18723 | 1.91e-05 | 4.52e-04 | 10 |
| GO:00344705 | Breast | Precancer | ncRNA processing | 42/1080 | 395/18723 | 9.91e-05 | 1.83e-03 | 42 |
| GO:00311004 | Breast | Precancer | animal organ regeneration | 14/1080 | 76/18723 | 9.92e-05 | 1.83e-03 | 14 |
| GO:00018898 | Breast | Precancer | liver development | 21/1080 | 147/18723 | 1.08e-04 | 1.96e-03 | 21 |
| GO:00610088 | Breast | Precancer | hepaticobiliary system development | 21/1080 | 150/18723 | 1.45e-04 | 2.49e-03 | 21 |
| GO:00310995 | Breast | Precancer | regeneration | 25/1080 | 198/18723 | 1.91e-04 | 3.06e-03 | 25 |
| GO:00346604 | Breast | Precancer | ncRNA metabolic process | 45/1080 | 485/18723 | 1.15e-03 | 1.26e-02 | 45 |
| GO:19908303 | Breast | Precancer | cellular response to leukemia inhibitory factor | 13/1080 | 94/18723 | 2.83e-03 | 2.49e-02 | 13 |
| GO:19908233 | Breast | Precancer | response to leukemia inhibitory factor | 13/1080 | 95/18723 | 3.11e-03 | 2.64e-02 | 13 |
| GO:00304902 | Breast | Precancer | maturation of SSU-rRNA | 8/1080 | 50/18723 | 7.39e-03 | 4.90e-02 | 8 |
| 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:004225414 | Breast | IDC | ribosome biogenesis | 52/1434 | 299/18723 | 1.90e-08 | 1.32e-06 | 52 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 |
| 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 |
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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 |
| RPS16 | SNV | Missense_Mutation | c.139C>G | p.Leu47Val | p.L47V | P62249 | protein_coding | deleterious(0.02) | probably_damaging(0.926) | TCGA-E2-A15L-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| RPS16 | SNV | Missense_Mutation | novel | c.176N>A | p.Gly59Asp | p.G59D | P62249 | protein_coding | deleterious(0.03) | possibly_damaging(0.686) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RPS16 | SNV | Missense_Mutation | novel | c.254G>A | p.Arg85His | p.R85H | P62249 | protein_coding | deleterious(0.02) | possibly_damaging(0.907) | TCGA-B5-A3FC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RPS16 | SNV | Missense_Mutation | c.163G>A | p.Val55Ile | p.V55I | P62249 | protein_coding | tolerated(0.73) | benign(0.029) | TCGA-BS-A0UF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RPS16 | SNV | Missense_Mutation | novel | c.206N>A | p.Arg69His | p.R69H | P62249 | protein_coding | tolerated(0.05) | benign(0.106) | TCGA-D1-A103-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RPS16 | SNV | Missense_Mutation | novel | c.253N>T | p.Arg85Cys | p.R85C | P62249 | protein_coding | deleterious(0.04) | possibly_damaging(0.797) | TCGA-D1-A16X-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RPS16 | SNV | Missense_Mutation | novel | c.49N>G | p.Lys17Glu | p.K17E | P62249 | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-EY-A1GI-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RPS16 | SNV | Missense_Mutation | c.346G>T | p.Asp116Tyr | p.D116Y | P62249 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-53-7624-01 | Lung | lung adenocarcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | PD | |
| RPS16 | SNV | Missense_Mutation | novel | c.205N>T | p.Arg69Cys | p.R69C | P62249 | protein_coding | deleterious(0.04) | benign(0.294) | TCGA-77-A5GA-01 | Lung | lung squamous cell carcinoma | Male | >=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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