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Gene: MRPS28 |
Gene summary for MRPS28 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | MRPS28 | Gene ID | 28957 |
| Gene name | mitochondrial ribosomal protein S28 | |
| Gene Alias | COXPD47 | |
| Cytomap | 8q21.13 | |
| Gene Type | protein-coding | GO ID | GO:0006412 | UniProtAcc | A0A0S2Z563 |
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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 |
| 28957 | MRPS28 | LZE2T | Human | Esophagus | ESCC | 4.95e-05 | 7.01e-01 | 0.082 |
| 28957 | MRPS28 | LZE4T | Human | Esophagus | ESCC | 4.81e-23 | 7.01e-01 | 0.0811 |
| 28957 | MRPS28 | LZE5T | Human | Esophagus | ESCC | 2.79e-03 | 3.64e-01 | 0.0514 |
| 28957 | MRPS28 | LZE7T | Human | Esophagus | ESCC | 7.00e-08 | 2.25e-01 | 0.0667 |
| 28957 | MRPS28 | LZE8T | Human | Esophagus | ESCC | 2.11e-15 | 5.50e-01 | 0.067 |
| 28957 | MRPS28 | LZE20T | Human | Esophagus | ESCC | 7.90e-16 | 6.36e-01 | 0.0662 |
| 28957 | MRPS28 | LZE22D1 | Human | Esophagus | HGIN | 2.44e-03 | 1.80e-01 | 0.0595 |
| 28957 | MRPS28 | LZE22T | Human | Esophagus | ESCC | 6.92e-08 | 3.64e-01 | 0.068 |
| 28957 | MRPS28 | LZE24T | Human | Esophagus | ESCC | 1.04e-19 | 5.83e-01 | 0.0596 |
| 28957 | MRPS28 | LZE21T | Human | Esophagus | ESCC | 2.22e-08 | 4.90e-01 | 0.0655 |
| 28957 | MRPS28 | LZE6T | Human | Esophagus | ESCC | 1.27e-07 | 4.53e-01 | 0.0845 |
| 28957 | MRPS28 | P1T-E | Human | Esophagus | ESCC | 9.88e-10 | 6.48e-01 | 0.0875 |
| 28957 | MRPS28 | P2T-E | Human | Esophagus | ESCC | 6.23e-35 | 7.34e-01 | 0.1177 |
| 28957 | MRPS28 | P4T-E | Human | Esophagus | ESCC | 6.22e-52 | 1.24e+00 | 0.1323 |
| 28957 | MRPS28 | P5T-E | Human | Esophagus | ESCC | 4.68e-43 | 8.54e-01 | 0.1327 |
| 28957 | MRPS28 | P8T-E | Human | Esophagus | ESCC | 1.34e-34 | 6.81e-01 | 0.0889 |
| 28957 | MRPS28 | P9T-E | Human | Esophagus | ESCC | 7.86e-34 | 7.49e-01 | 0.1131 |
| 28957 | MRPS28 | P10T-E | Human | Esophagus | ESCC | 1.25e-39 | 6.36e-01 | 0.116 |
| 28957 | MRPS28 | P11T-E | Human | Esophagus | ESCC | 3.85e-25 | 8.53e-01 | 0.1426 |
| 28957 | MRPS28 | P12T-E | Human | Esophagus | ESCC | 3.45e-68 | 1.24e+00 | 0.1122 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ |
| ∗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:00325435 | Esophagus | HGIN | mitochondrial translation | 23/2587 | 76/18723 | 1.61e-04 | 3.16e-03 | 23 |
| GO:01400534 | Esophagus | HGIN | mitochondrial gene expression | 27/2587 | 108/18723 | 1.34e-03 | 1.57e-02 | 27 |
| GO:014005313 | Esophagus | ESCC | mitochondrial gene expression | 93/8552 | 108/18723 | 1.96e-18 | 2.03e-16 | 93 |
| GO:003254314 | Esophagus | ESCC | mitochondrial translation | 68/8552 | 76/18723 | 1.02e-15 | 6.86e-14 | 68 |
| GO:0032543 | Liver | Cirrhotic | mitochondrial translation | 40/4634 | 76/18723 | 1.61e-07 | 4.29e-06 | 40 |
| GO:0140053 | Liver | Cirrhotic | mitochondrial gene expression | 49/4634 | 108/18723 | 2.35e-06 | 4.31e-05 | 49 |
| GO:01400531 | Liver | HCC | mitochondrial gene expression | 82/7958 | 108/18723 | 1.49e-12 | 7.20e-11 | 82 |
| GO:00325431 | Liver | HCC | mitochondrial translation | 62/7958 | 76/18723 | 2.95e-12 | 1.34e-10 | 62 |
| GO:01400533 | Oral cavity | OSCC | mitochondrial gene expression | 78/7305 | 108/18723 | 2.37e-12 | 9.86e-11 | 78 |
| GO:00325434 | Oral cavity | OSCC | mitochondrial translation | 59/7305 | 76/18723 | 7.21e-12 | 2.70e-10 | 59 |
| GO:003254313 | Oral cavity | LP | mitochondrial translation | 43/4623 | 76/18723 | 2.85e-09 | 1.26e-07 | 43 |
| GO:014005312 | Oral cavity | LP | mitochondrial gene expression | 53/4623 | 108/18723 | 3.54e-08 | 1.27e-06 | 53 |
| GO:00325436 | Skin | cSCC | mitochondrial translation | 47/4864 | 76/18723 | 4.70e-11 | 2.22e-09 | 47 |
| GO:01400535 | Skin | cSCC | mitochondrial gene expression | 56/4864 | 108/18723 | 8.06e-09 | 2.56e-07 | 56 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| MRPS28 | SNV | Missense_Mutation | c.233A>G | p.Glu78Gly | p.E78G | Q9Y2Q9 | protein_coding | deleterious(0.01) | possibly_damaging(0.795) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
| MRPS28 | SNV | Missense_Mutation | rs564912429 | c.151G>A | p.Gly51Ser | p.G51S | Q9Y2Q9 | protein_coding | deleterious(0.03) | benign(0.37) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| MRPS28 | SNV | Missense_Mutation | novel | c.71G>T | p.Arg24Met | p.R24M | Q9Y2Q9 | protein_coding | deleterious(0) | benign(0.07) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| MRPS28 | SNV | Missense_Mutation | novel | c.98N>A | p.Ser33Asn | p.S33N | Q9Y2Q9 | protein_coding | tolerated(0.09) | benign(0.227) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
| MRPS28 | SNV | Missense_Mutation | novel | c.505N>A | p.Leu169Ile | p.L169I | Q9Y2Q9 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AP-A1E0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | SD |
| MRPS28 | deletion | Frame_Shift_Del | novel | c.227delA | p.Asn76MetfsTer9 | p.N76Mfs*9 | Q9Y2Q9 | protein_coding | TCGA-AX-A2HD-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | ||
| MRPS28 | SNV | Missense_Mutation | novel | c.410N>T | p.Gly137Val | p.G137V | Q9Y2Q9 | protein_coding | deleterious(0) | probably_damaging(0.913) | TCGA-44-5644-01 | Lung | lung adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| MRPS28 | SNV | Missense_Mutation | novel | c.41G>T | p.Ser14Ile | p.S14I | Q9Y2Q9 | protein_coding | deleterious_low_confidence(0) | benign(0.143) | TCGA-55-8089-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| MRPS28 | SNV | Missense_Mutation | rs180680255 | c.209N>G | p.Gln70Arg | p.Q70R | Q9Y2Q9 | protein_coding | tolerated(0.65) | benign(0) | TCGA-69-7979-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| MRPS28 | SNV | Missense_Mutation | novel | c.278G>T | p.Gly93Val | p.G93V | Q9Y2Q9 | protein_coding | deleterious(0.04) | probably_damaging(1) | TCGA-34-8455-01 | Lung | lung squamous cell carcinoma | Male | >=65 | III/IV | Unknown | Unknown | PD |
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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 |
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