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Gene: RPS21 |
Gene summary for RPS21 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RPS21 | Gene ID | 6227 |
| Gene name | ribosomal protein S21 | |
| Gene Alias | HLDF | |
| Cytomap | 20q13.33 | |
| Gene Type | protein-coding | GO ID | GO:0000447 | UniProtAcc | P63220 |
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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 |
| 6227 | RPS21 | GSM4909281 | Human | Breast | IDC | 1.94e-18 | -2.81e-01 | 0.21 |
| 6227 | RPS21 | GSM4909286 | Human | Breast | IDC | 4.29e-02 | 1.16e-01 | 0.1081 |
| 6227 | RPS21 | GSM4909289 | Human | Breast | IDC | 4.63e-02 | -3.48e-01 | 0.1064 |
| 6227 | RPS21 | GSM4909290 | Human | Breast | IDC | 6.07e-24 | -5.01e-01 | 0.2096 |
| 6227 | RPS21 | GSM4909291 | Human | Breast | IDC | 2.45e-05 | -2.75e-01 | 0.1753 |
| 6227 | RPS21 | GSM4909294 | Human | Breast | IDC | 2.25e-10 | -3.84e-01 | 0.2022 |
| 6227 | RPS21 | GSM4909297 | Human | Breast | IDC | 1.12e-02 | -7.20e-02 | 0.1517 |
| 6227 | RPS21 | GSM4909298 | Human | Breast | IDC | 2.08e-03 | 1.35e-01 | 0.1551 |
| 6227 | RPS21 | GSM4909301 | Human | Breast | IDC | 6.36e-03 | 1.26e-01 | 0.1577 |
| 6227 | RPS21 | GSM4909303 | Human | Breast | IDC | 8.37e-06 | 2.47e-01 | 0.0438 |
| 6227 | RPS21 | GSM4909304 | Human | Breast | IDC | 6.08e-53 | 3.62e-01 | 0.1636 |
| 6227 | RPS21 | GSM4909305 | Human | Breast | IDC | 1.19e-08 | -2.69e-01 | 0.0436 |
| 6227 | RPS21 | GSM4909306 | Human | Breast | IDC | 6.18e-39 | -4.18e-01 | 0.1564 |
| 6227 | RPS21 | GSM4909307 | Human | Breast | IDC | 3.40e-23 | -3.43e-01 | 0.1569 |
| 6227 | RPS21 | GSM4909308 | Human | Breast | IDC | 1.52e-56 | -5.93e-01 | 0.158 |
| 6227 | RPS21 | GSM4909309 | Human | Breast | IDC | 7.47e-05 | -2.88e-01 | 0.0483 |
| 6227 | RPS21 | GSM4909311 | Human | Breast | IDC | 3.42e-18 | 8.88e-02 | 0.1534 |
| 6227 | RPS21 | GSM4909315 | Human | Breast | IDC | 5.49e-09 | 1.65e-01 | 0.21 |
| 6227 | RPS21 | GSM4909316 | Human | Breast | IDC | 3.38e-04 | 1.97e-01 | 0.21 |
| 6227 | RPS21 | GSM4909317 | Human | Breast | IDC | 1.10e-04 | 1.44e-01 | 0.1355 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 |
| 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:00344705 | Breast | Precancer | ncRNA processing | 42/1080 | 395/18723 | 9.91e-05 | 1.83e-03 | 42 |
| GO:00346604 | Breast | Precancer | ncRNA metabolic process | 45/1080 | 485/18723 | 1.15e-03 | 1.26e-02 | 45 |
| 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 |
| GO:004227414 | Breast | IDC | ribosomal small subunit biogenesis | 21/1434 | 73/18723 | 7.23e-08 | 4.42e-06 | 21 |
| GO:000636414 | Breast | IDC | rRNA processing | 35/1434 | 225/18723 | 4.59e-05 | 1.03e-03 | 35 |
| GO:001607214 | Breast | IDC | rRNA metabolic process | 36/1434 | 236/18723 | 5.48e-05 | 1.17e-03 | 36 |
| 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:002261324 | Breast | DCIS | ribonucleoprotein complex biogenesis | 83/1390 | 463/18723 | 3.65e-14 | 1.09e-11 | 83 |
| GO:004225423 | Breast | DCIS | ribosome biogenesis | 52/1390 | 299/18723 | 6.73e-09 | 5.44e-07 | 52 |
| GO:004227424 | Breast | DCIS | ribosomal small subunit biogenesis | 21/1390 | 73/18723 | 4.24e-08 | 2.67e-06 | 21 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 |
| 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 |
| RPS21 | SNV | Missense_Mutation | c.178N>T | p.Arg60Cys | p.R60C | P63220 | protein_coding | tolerated(0.05) | benign(0.141) | TCGA-LP-A4AV-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| RPS21 | SNV | Missense_Mutation | novel | c.64C>G | p.Arg22Gly | p.R22G | P63220 | protein_coding | deleterious(0) | possibly_damaging(0.755) | TCGA-VS-A959-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD |
| RPS21 | SNV | Missense_Mutation | novel | c.137T>G | p.Phe46Cys | p.F46C | P63220 | protein_coding | deleterious(0.01) | possibly_damaging(0.552) | TCGA-EI-6917-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5fluorouracil+oxaciplatina+l-folinian | SD |
| RPS21 | SNV | Missense_Mutation | novel | c.243N>T | p.Lys81Asn | p.K81N | P63220 | protein_coding | tolerated(0.05) | benign(0.057) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RPS21 | SNV | Missense_Mutation | c.122A>C | p.Lys41Thr | p.K41T | P63220 | protein_coding | tolerated(0.12) | benign(0.121) | TCGA-B5-A0JY-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD | |
| RPS21 | SNV | Missense_Mutation | rs528034127 | c.223G>A | p.Ala75Thr | p.A75T | P63220 | protein_coding | tolerated(0.24) | benign(0) | TCGA-B5-A3FA-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RPS21 | SNV | Missense_Mutation | novel | c.187N>A | p.Gly63Ser | p.G63S | P63220 | protein_coding | deleterious(0.01) | probably_damaging(0.993) | TCGA-22-1002-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| RPS21 | SNV | Missense_Mutation | c.232N>T | p.Ile78Phe | p.I78F | P63220 | protein_coding | tolerated(0.09) | benign(0.221) | TCGA-22-5477-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| RPS21 | SNV | Missense_Mutation | novel | c.98N>G | p.Gln33Arg | p.Q33R | P63220 | protein_coding | deleterious(0) | benign(0.084) | TCGA-HF-A5NB-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | fluorouracil | SD |
| RPS21 | deletion | In_Frame_Del | novel | c.131_166delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | p.Arg45_Cys56del | p.R45_C56del | P63220 | protein_coding | TCGA-HU-A4H5-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Chemotherapy | doxifluridine | 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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