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Gene: REXO4 |
Gene summary for REXO4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | REXO4 | Gene ID | 57109 |
| Gene name | REX4 homolog, 3'-5' exonuclease | |
| Gene Alias | REX4 | |
| Cytomap | 9q34.2 | |
| Gene Type | protein-coding | GO ID | GO:0000737 | UniProtAcc | B4E331 |
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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 |
| 57109 | REXO4 | LZE20T | Human | Esophagus | ESCC | 1.24e-06 | 2.27e-01 | 0.0662 |
| 57109 | REXO4 | LZE24T | Human | Esophagus | ESCC | 6.32e-12 | 3.29e-01 | 0.0596 |
| 57109 | REXO4 | P1T-E | Human | Esophagus | ESCC | 2.37e-02 | 1.78e-01 | 0.0875 |
| 57109 | REXO4 | P2T-E | Human | Esophagus | ESCC | 1.87e-25 | 4.47e-01 | 0.1177 |
| 57109 | REXO4 | P4T-E | Human | Esophagus | ESCC | 2.61e-07 | 2.35e-01 | 0.1323 |
| 57109 | REXO4 | P5T-E | Human | Esophagus | ESCC | 1.65e-07 | 1.75e-01 | 0.1327 |
| 57109 | REXO4 | P8T-E | Human | Esophagus | ESCC | 4.42e-22 | 3.93e-01 | 0.0889 |
| 57109 | REXO4 | P9T-E | Human | Esophagus | ESCC | 1.26e-06 | 1.51e-01 | 0.1131 |
| 57109 | REXO4 | P10T-E | Human | Esophagus | ESCC | 1.34e-17 | 2.57e-01 | 0.116 |
| 57109 | REXO4 | P11T-E | Human | Esophagus | ESCC | 1.26e-08 | 3.96e-01 | 0.1426 |
| 57109 | REXO4 | P12T-E | Human | Esophagus | ESCC | 5.56e-10 | 1.99e-01 | 0.1122 |
| 57109 | REXO4 | P15T-E | Human | Esophagus | ESCC | 1.99e-14 | 2.97e-01 | 0.1149 |
| 57109 | REXO4 | P16T-E | Human | Esophagus | ESCC | 9.12e-07 | 2.21e-01 | 0.1153 |
| 57109 | REXO4 | P17T-E | Human | Esophagus | ESCC | 5.95e-05 | 3.00e-01 | 0.1278 |
| 57109 | REXO4 | P20T-E | Human | Esophagus | ESCC | 3.83e-09 | 2.12e-01 | 0.1124 |
| 57109 | REXO4 | P21T-E | Human | Esophagus | ESCC | 9.86e-22 | 4.95e-01 | 0.1617 |
| 57109 | REXO4 | P22T-E | Human | Esophagus | ESCC | 4.75e-14 | 3.06e-01 | 0.1236 |
| 57109 | REXO4 | P23T-E | Human | Esophagus | ESCC | 1.46e-12 | 3.12e-01 | 0.108 |
| 57109 | REXO4 | P24T-E | Human | Esophagus | ESCC | 1.77e-18 | 3.78e-01 | 0.1287 |
| 57109 | REXO4 | P26T-E | Human | Esophagus | ESCC | 1.20e-14 | 2.58e-01 | 0.1276 |
| Page: 1 2 3 4 5 |
| 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:0022613111 | Esophagus | ESCC | ribonucleoprotein complex biogenesis | 365/8552 | 463/18723 | 1.74e-49 | 1.11e-45 | 365 |
| GO:0042254111 | Esophagus | ESCC | ribosome biogenesis | 252/8552 | 299/18723 | 3.27e-44 | 1.04e-40 | 252 |
| GO:003447015 | Esophagus | ESCC | ncRNA processing | 300/8552 | 395/18723 | 3.09e-35 | 3.26e-32 | 300 |
| GO:0016072110 | Esophagus | ESCC | rRNA metabolic process | 197/8552 | 236/18723 | 1.31e-33 | 1.18e-30 | 197 |
| GO:0006364110 | Esophagus | ESCC | rRNA processing | 189/8552 | 225/18723 | 4.88e-33 | 3.87e-30 | 189 |
| GO:003466012 | Esophagus | ESCC | ncRNA metabolic process | 346/8552 | 485/18723 | 4.35e-31 | 2.51e-28 | 346 |
| GO:0034655110 | Esophagus | ESCC | nucleobase-containing compound catabolic process | 272/8552 | 407/18723 | 2.92e-18 | 2.90e-16 | 272 |
| 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:00903053 | Esophagus | ESCC | nucleic acid phosphodiester bond hydrolysis | 163/8552 | 261/18723 | 3.07e-08 | 5.73e-07 | 163 |
| GO:002261322 | Liver | HCC | ribonucleoprotein complex biogenesis | 355/7958 | 463/18723 | 7.76e-52 | 4.92e-48 | 355 |
| GO:004225422 | Liver | HCC | ribosome biogenesis | 246/7958 | 299/18723 | 4.99e-46 | 1.58e-42 | 246 |
| GO:00344702 | Liver | HCC | ncRNA processing | 293/7958 | 395/18723 | 4.26e-38 | 6.76e-35 | 293 |
| GO:001607212 | Liver | HCC | rRNA metabolic process | 193/7958 | 236/18723 | 1.26e-35 | 1.14e-32 | 193 |
| GO:000636421 | Liver | HCC | rRNA processing | 185/7958 | 225/18723 | 8.14e-35 | 6.45e-32 | 185 |
| GO:00346601 | Liver | HCC | ncRNA metabolic process | 332/7958 | 485/18723 | 1.48e-31 | 7.80e-29 | 332 |
| GO:004427021 | Liver | HCC | cellular nitrogen compound catabolic process | 303/7958 | 451/18723 | 9.76e-27 | 3.64e-24 | 303 |
| GO:004670021 | Liver | HCC | heterocycle catabolic process | 299/7958 | 445/18723 | 2.07e-26 | 7.29e-24 | 299 |
| Page: 1 2 3 4 |
| 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 |
| REXO4 | insertion | Frame_Shift_Ins | novel | c.414_415insAAAATACAAAAAATTA | p.Asp139LysfsTer23 | p.D139Kfs*23 | Q9GZR2 | protein_coding | TCGA-B6-A0IN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | ||
| REXO4 | insertion | Frame_Shift_Ins | novel | c.412_413insAACCCCGTATCTAC | p.Met138LysfsTer76 | p.M138Kfs*76 | Q9GZR2 | protein_coding | TCGA-B6-A0IN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | ||
| REXO4 | SNV | Missense_Mutation | rs377306235 | c.437N>A | p.Arg146His | p.R146H | Q9GZR2 | protein_coding | tolerated(0.21) | benign(0) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| REXO4 | SNV | Missense_Mutation | c.599N>G | p.Asp200Gly | p.D200G | Q9GZR2 | protein_coding | deleterious(0.02) | benign(0.263) | TCGA-AA-3715-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| REXO4 | SNV | Missense_Mutation | novel | c.425N>T | p.Ala142Val | p.A142V | Q9GZR2 | protein_coding | tolerated(0.53) | benign(0) | TCGA-AA-3949-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| REXO4 | SNV | Missense_Mutation | c.853N>T | p.Pro285Ser | p.P285S | Q9GZR2 | protein_coding | deleterious(0.04) | benign(0.18) | TCGA-AD-A5EK-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| REXO4 | SNV | Missense_Mutation | c.1115T>G | p.Leu372Arg | p.L372R | Q9GZR2 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-AZ-4313-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| REXO4 | SNV | Missense_Mutation | novel | c.1045A>G | p.Lys349Glu | p.K349E | Q9GZR2 | protein_coding | deleterious(0) | possibly_damaging(0.475) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| REXO4 | SNV | Missense_Mutation | novel | c.245N>A | p.Ser82Tyr | p.S82Y | Q9GZR2 | protein_coding | deleterious(0.01) | possibly_damaging(0.453) | TCGA-A5-A2K5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| REXO4 | SNV | Missense_Mutation | novel | c.613G>A | p.Glu205Lys | p.E205K | Q9GZR2 | protein_coding | deleterious(0) | probably_damaging(0.967) | TCGA-AP-A056-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
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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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