|
|||||
|
 | |
| |
| |
| |
| |
| |
|
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 |
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 |
| 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. |
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:003139630 | Thyroid | HT | regulation of protein ubiquitination | 36/1272 | 210/18723 | 2.39e-07 | 1.19e-05 | 36 |
| GO:003311929 | Thyroid | HT | negative regulation of RNA splicing | 11/1272 | 25/18723 | 2.50e-07 | 1.21e-05 | 11 |
| GO:190179830 | Thyroid | HT | positive regulation of signal transduction by p53 class mediator | 11/1272 | 25/18723 | 2.50e-07 | 1.21e-05 | 11 |
| GO:190332130 | Thyroid | HT | negative regulation of protein modification by small protein conjugation or removal | 21/1272 | 95/18723 | 1.21e-06 | 4.73e-05 | 21 |
| GO:000002830 | Thyroid | HT | ribosomal small subunit assembly | 9/1272 | 19/18723 | 1.49e-06 | 5.66e-05 | 9 |
| GO:003139730 | Thyroid | HT | negative regulation of protein ubiquitination | 19/1272 | 83/18723 | 2.21e-06 | 7.82e-05 | 19 |
| GO:190179630 | Thyroid | HT | regulation of signal transduction by p53 class mediator | 20/1272 | 93/18723 | 3.39e-06 | 1.13e-04 | 20 |
| GO:200011629 | Thyroid | HT | regulation of cysteine-type endopeptidase activity | 36/1272 | 235/18723 | 3.74e-06 | 1.23e-04 | 36 |
| GO:190466730 | Thyroid | HT | negative regulation of ubiquitin protein ligase activity | 7/1272 | 12/18723 | 3.84e-06 | 1.25e-04 | 7 |
| GO:003410130 | Thyroid | HT | erythrocyte homeostasis | 24/1272 | 129/18723 | 5.57e-06 | 1.68e-04 | 24 |
| GO:000226230 | Thyroid | HT | myeloid cell homeostasis | 27/1272 | 157/18723 | 6.97e-06 | 2.01e-04 | 27 |
| GO:007233229 | Thyroid | HT | intrinsic apoptotic signaling pathway by p53 class mediator | 17/1272 | 76/18723 | 1.04e-05 | 2.81e-04 | 17 |
| GO:004328129 | Thyroid | HT | regulation of cysteine-type endopeptidase activity involved in apoptotic process | 32/1272 | 209/18723 | 1.29e-05 | 3.31e-04 | 32 |
| GO:005144430 | Thyroid | HT | negative regulation of ubiquitin-protein transferase activity | 8/1272 | 19/18723 | 1.71e-05 | 4.11e-04 | 8 |
| GO:004887230 | Thyroid | HT | homeostasis of number of cells | 38/1272 | 272/18723 | 1.82e-05 | 4.31e-04 | 38 |
| GO:001095228 | Thyroid | HT | positive regulation of peptidase activity | 30/1272 | 197/18723 | 2.63e-05 | 5.84e-04 | 30 |
| GO:000636425 | Thyroid | HT | rRNA processing | 32/1272 | 225/18723 | 5.72e-05 | 1.10e-03 | 32 |
| GO:190466629 | Thyroid | HT | regulation of ubiquitin protein ligase activity | 8/1272 | 23/18723 | 8.66e-05 | 1.48e-03 | 8 |
| GO:001607225 | Thyroid | HT | rRNA metabolic process | 32/1272 | 236/18723 | 1.43e-04 | 2.21e-03 | 32 |
| GO:003406310 | Thyroid | HT | stress granule assembly | 8/1272 | 26/18723 | 2.30e-04 | 3.27e-03 | 8 |
| 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 |
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 |
| 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 |
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 |
| 6187 | RPS2 | NA | FGF3 | 16263090 |
| Page: 1 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |