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Gene: RPS2 |
Gene summary for RPS2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RPS2 | Gene ID | 6187 |
| Gene name | ribosomal protein S2 | |
| Gene Alias | LLREP3 | |
| Cytomap | 16p13.3 | |
| Gene Type | protein-coding | GO ID | GO:0002181 | UniProtAcc | P15880 |
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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 |
| 6187 | RPS2 | CCI_1 | Human | Cervix | CC | 2.56e-66 | -1.91e+00 | 0.528 |
| 6187 | RPS2 | CCI_2 | Human | Cervix | CC | 1.27e-33 | -1.09e+00 | 0.5249 |
| 6187 | RPS2 | CCI_3 | Human | Cervix | CC | 1.69e-62 | -1.79e+00 | 0.516 |
| 6187 | RPS2 | CCII_1 | Human | Cervix | CC | 4.20e-94 | -2.01e+00 | 0.3249 |
| 6187 | RPS2 | Tumor | Human | Cervix | CC | 7.87e-10 | -1.49e-01 | 0.1241 |
| 6187 | RPS2 | sample3 | Human | Cervix | CC | 1.88e-39 | -3.03e-01 | 0.1387 |
| 6187 | RPS2 | H2 | Human | Cervix | HSIL_HPV | 2.01e-56 | -5.69e-01 | 0.0632 |
| 6187 | RPS2 | T1 | Human | Cervix | CC | 6.50e-14 | -1.94e-01 | 0.0918 |
| 6187 | RPS2 | T2 | Human | Cervix | CC | 2.70e-05 | -2.25e-01 | 0.0709 |
| 6187 | RPS2 | T3 | Human | Cervix | CC | 3.73e-35 | -2.99e-01 | 0.1389 |
| 6187 | RPS2 | HTA11_3410_2000001011 | Human | Colorectum | AD | 8.02e-128 | 3.08e+00 | 0.0155 |
| 6187 | RPS2 | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.02e-63 | 3.96e+00 | -0.1808 |
| 6187 | RPS2 | HTA11_2951_2000001011 | Human | Colorectum | AD | 1.85e-37 | 4.33e+00 | 0.0216 |
| 6187 | RPS2 | HTA11_1938_2000001011 | Human | Colorectum | AD | 1.52e-65 | 3.88e+00 | -0.0811 |
| 6187 | RPS2 | HTA11_78_2000001011 | Human | Colorectum | AD | 3.20e-74 | 3.01e+00 | -0.1088 |
| 6187 | RPS2 | HTA11_347_2000001011 | Human | Colorectum | AD | 2.03e-96 | 3.93e+00 | -0.1954 |
| 6187 | RPS2 | HTA11_411_2000001011 | Human | Colorectum | SER | 7.92e-26 | 4.03e+00 | -0.2602 |
| 6187 | RPS2 | HTA11_2112_2000001011 | Human | Colorectum | SER | 8.65e-15 | 3.59e+00 | -0.2196 |
| 6187 | RPS2 | HTA11_3361_2000001011 | Human | Colorectum | AD | 9.53e-64 | 3.74e+00 | -0.1207 |
| 6187 | RPS2 | HTA11_83_2000001011 | Human | Colorectum | SER | 2.24e-50 | 3.53e+00 | -0.1526 |
| 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 |
| 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:00226139 | Breast | Precancer | ribonucleoprotein complex biogenesis | 79/1080 | 463/18723 | 2.11e-18 | 1.03e-15 | 79 |
| GO:00971939 | Breast | Precancer | intrinsic apoptotic signaling pathway | 59/1080 | 288/18723 | 8.07e-18 | 3.60e-15 | 59 |
| 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:00525479 | Breast | Precancer | regulation of peptidase activity | 71/1080 | 461/18723 | 2.72e-14 | 6.94e-12 | 71 |
| GO:00525489 | Breast | Precancer | regulation of endopeptidase activity | 67/1080 | 432/18723 | 1.06e-13 | 2.36e-11 | 67 |
| GO:00422549 | Breast | Precancer | ribosome biogenesis | 52/1080 | 299/18723 | 7.35e-13 | 1.51e-10 | 52 |
| GO:00083809 | Breast | Precancer | RNA splicing | 65/1080 | 434/18723 | 1.27e-12 | 2.53e-10 | 65 |
| GO:00434849 | Breast | Precancer | regulation of RNA splicing | 34/1080 | 148/18723 | 2.66e-12 | 4.75e-10 | 34 |
| GO:00064179 | Breast | Precancer | regulation of translation | 67/1080 | 468/18723 | 4.71e-12 | 7.64e-10 | 67 |
| GO:00457279 | Breast | Precancer | positive regulation of translation | 32/1080 | 136/18723 | 5.89e-12 | 9.27e-10 | 32 |
| GO:00422559 | Breast | Precancer | ribosome assembly | 21/1080 | 61/18723 | 1.06e-11 | 1.53e-09 | 21 |
| GO:20001169 | Breast | Precancer | regulation of cysteine-type endopeptidase activity | 43/1080 | 235/18723 | 1.30e-11 | 1.83e-09 | 43 |
| GO:00432819 | Breast | Precancer | regulation of cysteine-type endopeptidase activity involved in apoptotic process | 40/1080 | 209/18723 | 1.59e-11 | 2.07e-09 | 40 |
| GO:00342509 | Breast | Precancer | positive regulation of cellular amide metabolic process | 33/1080 | 162/18723 | 1.72e-10 | 1.77e-08 | 33 |
| GO:00422749 | Breast | Precancer | ribosomal small subunit biogenesis | 21/1080 | 73/18723 | 4.84e-10 | 4.39e-08 | 21 |
| GO:00458629 | Breast | Precancer | positive regulation of proteolysis | 51/1080 | 372/18723 | 7.77e-09 | 5.70e-07 | 51 |
| GO:19033209 | Breast | Precancer | regulation of protein modification by small protein conjugation or removal | 38/1080 | 242/18723 | 1.71e-08 | 1.17e-06 | 38 |
| GO:00000289 | Breast | Precancer | ribosomal small subunit assembly | 10/1080 | 19/18723 | 2.24e-08 | 1.50e-06 | 10 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0517120 | Cervix | CC | Coronavirus disease - COVID-19 | 111/1267 | 232/8465 | 1.82e-33 | 5.90e-31 | 3.49e-31 | 111 |
| hsa05171110 | Cervix | CC | Coronavirus disease - COVID-19 | 111/1267 | 232/8465 | 1.82e-33 | 5.90e-31 | 3.49e-31 | 111 |
| 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 |
| hsa03010 | Colorectum | AD | Ribosome | 96/2092 | 167/8465 | 8.28e-20 | 5.54e-18 | 3.54e-18 | 96 |
| hsa05171 | Colorectum | AD | Coronavirus disease - COVID-19 | 113/2092 | 232/8465 | 9.90e-16 | 2.55e-14 | 1.63e-14 | 113 |
| hsa030101 | Colorectum | AD | Ribosome | 96/2092 | 167/8465 | 8.28e-20 | 5.54e-18 | 3.54e-18 | 96 |
| hsa051711 | Colorectum | AD | Coronavirus disease - COVID-19 | 113/2092 | 232/8465 | 9.90e-16 | 2.55e-14 | 1.63e-14 | 113 |
| hsa030102 | Colorectum | SER | Ribosome | 92/1580 | 167/8465 | 2.21e-26 | 3.66e-24 | 2.66e-24 | 92 |
| hsa051712 | Colorectum | SER | Coronavirus disease - COVID-19 | 98/1580 | 232/8465 | 3.33e-17 | 8.50e-16 | 6.17e-16 | 98 |
| hsa030103 | Colorectum | SER | Ribosome | 92/1580 | 167/8465 | 2.21e-26 | 3.66e-24 | 2.66e-24 | 92 |
| hsa051713 | Colorectum | SER | Coronavirus disease - COVID-19 | 98/1580 | 232/8465 | 3.33e-17 | 8.50e-16 | 6.17e-16 | 98 |
| hsa030104 | Colorectum | MSS | Ribosome | 96/1875 | 167/8465 | 1.82e-23 | 2.03e-21 | 1.24e-21 | 96 |
| hsa051714 | Colorectum | MSS | Coronavirus disease - COVID-19 | 108/1875 | 232/8465 | 6.50e-17 | 1.67e-15 | 1.03e-15 | 108 |
| hsa030105 | Colorectum | MSS | Ribosome | 96/1875 | 167/8465 | 1.82e-23 | 2.03e-21 | 1.24e-21 | 96 |
| hsa051715 | Colorectum | MSS | Coronavirus disease - COVID-19 | 108/1875 | 232/8465 | 6.50e-17 | 1.67e-15 | 1.03e-15 | 108 |
| hsa030106 | Colorectum | MSI-H | Ribosome | 87/797 | 167/8465 | 5.55e-46 | 1.80e-43 | 1.51e-43 | 87 |
| hsa051716 | Colorectum | MSI-H | Coronavirus disease - COVID-19 | 91/797 | 232/8465 | 2.21e-35 | 3.58e-33 | 3.00e-33 | 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 |
| RPS2 | SNV | Missense_Mutation | c.825N>C | p.Lys275Asn | p.K275N | P15880 | protein_coding | deleterious(0) | benign(0.142) | TCGA-BH-A1FC-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RPS2 | SNV | Missense_Mutation | novel | c.137G>C | p.Arg46Pro | p.R46P | P15880 | protein_coding | tolerated(0.23) | probably_damaging(0.969) | TCGA-C5-A1BK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| RPS2 | SNV | Missense_Mutation | c.620N>T | p.Ala207Val | p.A207V | P15880 | protein_coding | deleterious(0.05) | possibly_damaging(0.542) | TCGA-AD-6964-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | folfox | PD | |
| RPS2 | SNV | Missense_Mutation | c.728C>T | p.Ala243Val | p.A243V | P15880 | protein_coding | deleterious(0.02) | probably_damaging(0.974) | TCGA-CM-4743-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | capecitabine | SD | |
| RPS2 | SNV | Missense_Mutation | c.580C>T | p.Arg194Cys | p.R194C | P15880 | protein_coding | tolerated(0.19) | benign(0.168) | TCGA-G5-6233-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | 5-fluorouracil | PD | |
| RPS2 | SNV | Missense_Mutation | novel | c.362N>A | p.Arg121His | p.R121H | P15880 | protein_coding | deleterious(0.04) | benign(0.427) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RPS2 | SNV | Missense_Mutation | rs753906824 | c.820N>A | p.Val274Ile | p.V274I | P15880 | protein_coding | tolerated(0.22) | benign(0.074) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
| RPS2 | SNV | Missense_Mutation | novel | c.557N>A | p.Gly186Asp | p.G186D | P15880 | protein_coding | deleterious(0.01) | possibly_damaging(0.905) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
| RPS2 | SNV | Missense_Mutation | novel | c.341N>C | p.Lys114Thr | p.K114T | P15880 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
| RPS2 | SNV | Missense_Mutation | novel | c.655A>T | p.Ile219Phe | p.I219F | P15880 | protein_coding | deleterious(0.01) | benign(0.364) | TCGA-AJ-A3NE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 |
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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 |
| 6187 | RPS2 | NA | FGF3 | 16263090 |
| Page: 1 |
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