|
|||||
|
 | |
| |
| |
| |
| |
| |
|
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 |
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 |
| 28957 | MRPS28 | P89T-E | Human | Esophagus | ESCC | 2.99e-27 | 1.86e+00 | 0.1752 |
| 28957 | MRPS28 | P91T-E | Human | Esophagus | ESCC | 1.21e-27 | 2.04e+00 | 0.1828 |
| 28957 | MRPS28 | P94T-E | Human | Esophagus | ESCC | 1.18e-02 | 3.22e-01 | 0.0879 |
| 28957 | MRPS28 | P107T-E | Human | Esophagus | ESCC | 2.43e-58 | 1.16e+00 | 0.171 |
| 28957 | MRPS28 | P126T-E | Human | Esophagus | ESCC | 4.26e-11 | 9.24e-01 | 0.1125 |
| 28957 | MRPS28 | P127T-E | Human | Esophagus | ESCC | 1.88e-26 | 4.60e-01 | 0.0826 |
| 28957 | MRPS28 | P128T-E | Human | Esophagus | ESCC | 4.67e-64 | 1.89e+00 | 0.1241 |
| 28957 | MRPS28 | P130T-E | Human | Esophagus | ESCC | 4.45e-64 | 1.26e+00 | 0.1676 |
| 28957 | MRPS28 | HCC1_Meng | Human | Liver | HCC | 7.39e-84 | 4.02e-01 | 0.0246 |
| 28957 | MRPS28 | HCC2_Meng | Human | Liver | HCC | 4.11e-35 | 4.84e-02 | 0.0107 |
| 28957 | MRPS28 | cirrhotic1 | Human | Liver | Cirrhotic | 1.87e-09 | 2.50e-01 | 0.0202 |
| 28957 | MRPS28 | cirrhotic2 | Human | Liver | Cirrhotic | 3.94e-17 | 2.55e-01 | 0.0201 |
| 28957 | MRPS28 | cirrhotic3 | Human | Liver | Cirrhotic | 3.77e-17 | 2.62e-01 | 0.0215 |
| 28957 | MRPS28 | HCC2 | Human | Liver | HCC | 1.02e-04 | 2.75e+00 | 0.5341 |
| 28957 | MRPS28 | Pt13.b | Human | Liver | HCC | 2.68e-35 | 3.57e-01 | 0.0251 |
| 28957 | MRPS28 | Pt14.b | Human | Liver | HCC | 1.48e-04 | 1.70e-01 | 0.018 |
| 28957 | MRPS28 | S014 | Human | Liver | HCC | 1.48e-33 | 1.36e+00 | 0.2254 |
| 28957 | MRPS28 | S015 | Human | Liver | HCC | 1.99e-36 | 1.86e+00 | 0.2375 |
| 28957 | MRPS28 | S016 | Human | Liver | HCC | 9.39e-42 | 1.43e+00 | 0.2243 |
| 28957 | MRPS28 | S027 | Human | Liver | HCC | 3.11e-02 | 6.16e-01 | 0.2446 |
| Page: 1 2 3 4 5 6 |
| 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. |
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: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 |
| Page: 1 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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 |
| 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 |
| Page: 1 2 |
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 |
| Page: 1 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |