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Gene: MRPL4 |
Gene summary for MRPL4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | MRPL4 | Gene ID | 51073 |
| Gene name | mitochondrial ribosomal protein L4 | |
| Gene Alias | CGI-28 | |
| Cytomap | 19p13.2 | |
| Gene Type | protein-coding | GO ID | GO:0006412 | UniProtAcc | A0A024R7C5 |
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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 |
| 51073 | MRPL4 | LZE2T | Human | Esophagus | ESCC | 9.93e-09 | 1.08e+00 | 0.082 |
| 51073 | MRPL4 | LZE4T | Human | Esophagus | ESCC | 1.15e-11 | 4.91e-01 | 0.0811 |
| 51073 | MRPL4 | LZE5T | Human | Esophagus | ESCC | 3.59e-05 | 4.83e-01 | 0.0514 |
| 51073 | MRPL4 | LZE7T | Human | Esophagus | ESCC | 1.15e-21 | 1.45e+00 | 0.0667 |
| 51073 | MRPL4 | LZE8T | Human | Esophagus | ESCC | 1.22e-09 | 5.06e-01 | 0.067 |
| 51073 | MRPL4 | LZE20T | Human | Esophagus | ESCC | 3.92e-04 | 3.22e-01 | 0.0662 |
| 51073 | MRPL4 | LZE22D1 | Human | Esophagus | HGIN | 6.20e-03 | 2.25e-01 | 0.0595 |
| 51073 | MRPL4 | LZE22T | Human | Esophagus | ESCC | 1.91e-08 | 7.61e-01 | 0.068 |
| 51073 | MRPL4 | LZE24T | Human | Esophagus | ESCC | 3.10e-31 | 1.06e+00 | 0.0596 |
| 51073 | MRPL4 | LZE21T | Human | Esophagus | ESCC | 6.22e-07 | 8.31e-01 | 0.0655 |
| 51073 | MRPL4 | LZE6T | Human | Esophagus | ESCC | 1.19e-08 | 5.61e-01 | 0.0845 |
| 51073 | MRPL4 | P1T-E | Human | Esophagus | ESCC | 4.36e-20 | 1.08e+00 | 0.0875 |
| 51073 | MRPL4 | P2T-E | Human | Esophagus | ESCC | 9.94e-32 | 6.58e-01 | 0.1177 |
| 51073 | MRPL4 | P4T-E | Human | Esophagus | ESCC | 5.21e-57 | 1.52e+00 | 0.1323 |
| 51073 | MRPL4 | P5T-E | Human | Esophagus | ESCC | 6.25e-68 | 1.53e+00 | 0.1327 |
| 51073 | MRPL4 | P8T-E | Human | Esophagus | ESCC | 8.00e-57 | 1.23e+00 | 0.0889 |
| 51073 | MRPL4 | P9T-E | Human | Esophagus | ESCC | 3.39e-51 | 1.35e+00 | 0.1131 |
| 51073 | MRPL4 | P10T-E | Human | Esophagus | ESCC | 4.41e-66 | 1.07e+00 | 0.116 |
| 51073 | MRPL4 | P11T-E | Human | Esophagus | ESCC | 3.13e-23 | 1.05e+00 | 0.1426 |
| 51073 | MRPL4 | P12T-E | Human | Esophagus | ESCC | 3.86e-59 | 1.18e+00 | 0.1122 |
| Page: 1 2 3 4 5 6 7 |
| 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 | ||
| 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:00325432 | Breast | IDC | mitochondrial translation | 13/1434 | 76/18723 | 4.81e-03 | 3.67e-02 | 13 |
| GO:003254311 | Breast | DCIS | mitochondrial translation | 13/1390 | 76/18723 | 3.70e-03 | 2.99e-02 | 13 |
| 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:0016072110 | Esophagus | ESCC | rRNA metabolic process | 197/8552 | 236/18723 | 1.31e-33 | 1.18e-30 | 197 |
| GO:003466012 | Esophagus | ESCC | ncRNA metabolic process | 346/8552 | 485/18723 | 4.35e-31 | 2.51e-28 | 346 |
| GO:0006401110 | Esophagus | ESCC | RNA catabolic process | 204/8552 | 278/18723 | 3.39e-21 | 5.66e-19 | 204 |
| GO:014005313 | Esophagus | ESCC | mitochondrial gene expression | 93/8552 | 108/18723 | 1.96e-18 | 2.03e-16 | 93 |
| GO:0034655110 | Esophagus | ESCC | nucleobase-containing compound catabolic process | 272/8552 | 407/18723 | 2.92e-18 | 2.90e-16 | 272 |
| GO:003254314 | Esophagus | ESCC | mitochondrial translation | 68/8552 | 76/18723 | 1.02e-15 | 6.86e-14 | 68 |
| GO:004670018 | Esophagus | ESCC | heterocycle catabolic process | 286/8552 | 445/18723 | 1.12e-15 | 7.47e-14 | 286 |
| GO:004427019 | Esophagus | ESCC | cellular nitrogen compound catabolic process | 288/8552 | 451/18723 | 3.03e-15 | 1.79e-13 | 288 |
| GO:001943918 | Esophagus | ESCC | aromatic compound catabolic process | 295/8552 | 467/18723 | 1.09e-14 | 5.98e-13 | 295 |
| GO:190136118 | Esophagus | ESCC | organic cyclic compound catabolic process | 307/8552 | 495/18723 | 9.99e-14 | 4.80e-12 | 307 |
| GO:00905013 | Esophagus | ESCC | RNA phosphodiester bond hydrolysis | 110/8552 | 152/18723 | 1.95e-11 | 6.81e-10 | 110 |
| GO:00903053 | Esophagus | ESCC | nucleic acid phosphodiester bond hydrolysis | 163/8552 | 261/18723 | 3.07e-08 | 5.73e-07 | 163 |
| GO:000641419 | Esophagus | ESCC | translational elongation | 41/8552 | 55/18723 | 1.26e-05 | 1.16e-04 | 41 |
| GO:00346613 | Esophagus | ESCC | ncRNA catabolic process | 33/8552 | 43/18723 | 3.25e-05 | 2.69e-04 | 33 |
| GO:00905023 | Esophagus | ESCC | RNA phosphodiester bond hydrolysis, endonucleolytic | 55/8552 | 82/18723 | 7.34e-05 | 5.51e-04 | 55 |
| GO:00160752 | Esophagus | ESCC | rRNA catabolic process | 18/8552 | 21/18723 | 1.81e-04 | 1.16e-03 | 18 |
| Page: 1 2 3 4 5 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0301039 | Esophagus | HGIN | Ribosome | 108/1383 | 167/8465 | 1.44e-45 | 4.71e-43 | 3.74e-43 | 108 |
| hsa03010115 | Esophagus | HGIN | Ribosome | 108/1383 | 167/8465 | 1.44e-45 | 4.71e-43 | 3.74e-43 | 108 |
| hsa03010211 | Esophagus | ESCC | Ribosome | 129/4205 | 167/8465 | 1.43e-13 | 3.43e-12 | 1.75e-12 | 129 |
| hsa03010310 | Esophagus | ESCC | Ribosome | 129/4205 | 167/8465 | 1.43e-13 | 3.43e-12 | 1.75e-12 | 129 |
| hsa0301022 | Liver | Cirrhotic | Ribosome | 127/2530 | 167/8465 | 2.12e-35 | 7.06e-33 | 4.35e-33 | 127 |
| hsa0301032 | Liver | Cirrhotic | Ribosome | 127/2530 | 167/8465 | 2.12e-35 | 7.06e-33 | 4.35e-33 | 127 |
| hsa0301042 | Liver | HCC | Ribosome | 128/4020 | 167/8465 | 7.32e-15 | 2.23e-13 | 1.24e-13 | 128 |
| hsa0301052 | Liver | HCC | Ribosome | 128/4020 | 167/8465 | 7.32e-15 | 2.23e-13 | 1.24e-13 | 128 |
| hsa0301030 | Oral cavity | OSCC | Ribosome | 128/3704 | 167/8465 | 2.42e-18 | 1.62e-16 | 8.25e-17 | 128 |
| hsa03010114 | Oral cavity | OSCC | Ribosome | 128/3704 | 167/8465 | 2.42e-18 | 1.62e-16 | 8.25e-17 | 128 |
| hsa03010210 | Oral cavity | LP | Ribosome | 127/2418 | 167/8465 | 1.22e-37 | 4.05e-35 | 2.61e-35 | 127 |
| hsa0301038 | Oral cavity | LP | Ribosome | 127/2418 | 167/8465 | 1.22e-37 | 4.05e-35 | 2.61e-35 | 127 |
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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 |
| MRPL4 | SNV | Missense_Mutation | c.172C>G | p.His58Asp | p.H58D | Q9BYD3 | protein_coding | deleterious(0.05) | benign(0.095) | TCGA-AO-A0J9-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | PD | |
| MRPL4 | SNV | Missense_Mutation | rs755737882 | c.431N>T | p.Pro144Leu | p.P144L | Q9BYD3 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-BH-A1FU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
| MRPL4 | SNV | Missense_Mutation | novel | c.370G>A | p.Gly124Ser | p.G124S | Q9BYD3 | protein_coding | deleterious(0.03) | probably_damaging(0.98) | TCGA-VS-A8EJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
| MRPL4 | SNV | Missense_Mutation | novel | c.79G>C | p.Glu27Gln | p.E27Q | Q9BYD3 | protein_coding | tolerated(0.14) | benign(0.031) | TCGA-VS-A9UR-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
| MRPL4 | insertion | In_Frame_Ins | novel | c.129_130insACCTGG | p.Leu43_Pro44insThrTrp | p.L43_P44insTW | Q9BYD3 | protein_coding | TCGA-DS-A1OB-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | carboplatin | PD | ||
| MRPL4 | SNV | Missense_Mutation | rs753032227 | c.556N>A | p.Asp186Asn | p.D186N | Q9BYD3 | protein_coding | tolerated(0.15) | benign(0.262) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| MRPL4 | insertion | Frame_Shift_Ins | novel | c.131_132insT | p.Glu45GlyfsTer66 | p.E45Gfs*66 | Q9BYD3 | protein_coding | TCGA-AM-5820-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| MRPL4 | SNV | Missense_Mutation | novel | c.214T>G | p.Phe72Val | p.F72V | Q9BYD3 | protein_coding | tolerated(0.69) | benign(0) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| MRPL4 | SNV | Missense_Mutation | rs752119612 | c.425G>A | p.Arg142His | p.R142H | Q9BYD3 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-B5-A3FC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| MRPL4 | SNV | Missense_Mutation | rs753032227 | c.556G>A | p.Asp186Asn | p.D186N | Q9BYD3 | protein_coding | tolerated(0.15) | benign(0.262) | TCGA-B5-A3FC-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 |
| Page: 1 |
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