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Gene: DDX58 |
Gene summary for DDX58 |
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Gene information | Species | Human | Gene symbol | DDX58 | Gene ID | 23586 |
Gene name | DExD/H-box helicase 58 | |
Gene Alias | RIG-I | |
Cytomap | 9p21.1 | |
Gene Type | protein-coding | GO ID | GO:0001816 | UniProtAcc | O95786 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
23586 | DDX58 | CCI_2 | Human | Cervix | CC | 3.65e-12 | 1.94e+00 | 0.5249 |
23586 | DDX58 | CCI_3 | Human | Cervix | CC | 1.53e-03 | 5.44e-01 | 0.516 |
23586 | DDX58 | HTA11_347_2000001011 | Human | Colorectum | AD | 2.79e-07 | 3.08e-01 | -0.1954 |
23586 | DDX58 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 4.98e-02 | 2.30e-01 | 0.294 |
23586 | DDX58 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 2.98e-06 | 1.18e+00 | 0.3487 |
23586 | DDX58 | LZE4T | Human | Esophagus | ESCC | 6.43e-06 | 2.82e-01 | 0.0811 |
23586 | DDX58 | LZE5T | Human | Esophagus | ESCC | 2.36e-09 | 4.97e-01 | 0.0514 |
23586 | DDX58 | LZE7T | Human | Esophagus | ESCC | 1.91e-03 | 3.17e-01 | 0.0667 |
23586 | DDX58 | LZE20T | Human | Esophagus | ESCC | 7.63e-07 | 2.64e-01 | 0.0662 |
23586 | DDX58 | LZE21D1 | Human | Esophagus | HGIN | 1.60e-04 | 7.60e-01 | 0.0632 |
23586 | DDX58 | LZE24T | Human | Esophagus | ESCC | 3.23e-18 | 6.91e-01 | 0.0596 |
23586 | DDX58 | LZE21T | Human | Esophagus | ESCC | 1.94e-05 | 5.68e-01 | 0.0655 |
23586 | DDX58 | LZE6T | Human | Esophagus | ESCC | 3.20e-02 | 1.71e-01 | 0.0845 |
23586 | DDX58 | P1T-E | Human | Esophagus | ESCC | 3.45e-13 | 7.96e-01 | 0.0875 |
23586 | DDX58 | P2T-E | Human | Esophagus | ESCC | 1.24e-49 | 9.23e-01 | 0.1177 |
23586 | DDX58 | P4T-E | Human | Esophagus | ESCC | 4.65e-07 | 3.11e-01 | 0.1323 |
23586 | DDX58 | P5T-E | Human | Esophagus | ESCC | 5.12e-31 | 1.08e+00 | 0.1327 |
23586 | DDX58 | P8T-E | Human | Esophagus | ESCC | 3.52e-19 | 3.61e-01 | 0.0889 |
23586 | DDX58 | P9T-E | Human | Esophagus | ESCC | 5.12e-34 | 8.86e-01 | 0.1131 |
23586 | DDX58 | P11T-E | Human | Esophagus | ESCC | 2.01e-25 | 9.48e-01 | 0.1426 |
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∗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 |
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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). |
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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00027644 | Cervix | CC | immune response-regulating signaling pathway | 97/2311 | 468/18723 | 1.49e-07 | 7.07e-06 | 97 |
GO:00018197 | Cervix | CC | positive regulation of cytokine production | 95/2311 | 467/18723 | 4.88e-07 | 1.85e-05 | 95 |
GO:00305229 | Cervix | CC | intracellular receptor signaling pathway | 60/2311 | 265/18723 | 1.89e-06 | 5.97e-05 | 60 |
GO:00510904 | Cervix | CC | regulation of DNA-binding transcription factor activity | 87/2311 | 440/18723 | 4.85e-06 | 1.22e-04 | 87 |
GO:00028315 | Cervix | CC | regulation of response to biotic stimulus | 67/2311 | 327/18723 | 1.79e-05 | 3.36e-04 | 67 |
GO:00096158 | Cervix | CC | response to virus | 73/2311 | 367/18723 | 2.22e-05 | 3.95e-04 | 73 |
GO:00022212 | Cervix | CC | pattern recognition receptor signaling pathway | 39/2311 | 172/18723 | 1.08e-04 | 1.38e-03 | 39 |
GO:00027534 | Cervix | CC | cytoplasmic pattern recognition receptor signaling pathway | 18/2311 | 60/18723 | 2.26e-04 | 2.55e-03 | 18 |
GO:00510915 | Cervix | CC | positive regulation of DNA-binding transcription factor activity | 51/2311 | 260/18723 | 5.05e-04 | 4.92e-03 | 51 |
GO:00395292 | Cervix | CC | RIG-I signaling pathway | 10/2311 | 27/18723 | 9.25e-04 | 7.84e-03 | 10 |
GO:00026973 | Cervix | CC | regulation of immune effector process | 62/2311 | 339/18723 | 9.25e-04 | 7.84e-03 | 62 |
GO:00027201 | Cervix | CC | positive regulation of cytokine production involved in immune response | 17/2311 | 65/18723 | 1.84e-03 | 1.37e-02 | 17 |
GO:00985863 | Cervix | CC | cellular response to virus | 20/2311 | 84/18723 | 2.62e-03 | 1.81e-02 | 20 |
GO:0002443 | Cervix | CC | leukocyte mediated immunity | 73/2311 | 440/18723 | 5.01e-03 | 2.98e-02 | 73 |
GO:0002699 | Cervix | CC | positive regulation of immune effector process | 43/2311 | 235/18723 | 5.13e-03 | 3.02e-02 | 43 |
GO:00324791 | Cervix | CC | regulation of type I interferon production | 21/2311 | 95/18723 | 5.32e-03 | 3.10e-02 | 21 |
GO:00326061 | Cervix | CC | type I interferon production | 21/2311 | 95/18723 | 5.32e-03 | 3.10e-02 | 21 |
GO:00395281 | Cervix | CC | cytoplasmic pattern recognition receptor signaling pathway in response to virus | 10/2311 | 34/18723 | 6.40e-03 | 3.58e-02 | 10 |
GO:00607602 | Cervix | CC | positive regulation of response to cytokine stimulus | 14/2311 | 57/18723 | 8.17e-03 | 4.25e-02 | 14 |
GO:00324815 | Cervix | CC | positive regulation of type I interferon production | 14/2311 | 58/18723 | 9.57e-03 | 4.73e-02 | 14 |
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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 |
hsa0516920 | Cervix | CC | Epstein-Barr virus infection | 57/1267 | 202/8465 | 7.30e-07 | 7.39e-06 | 4.37e-06 | 57 |
hsa0516414 | Cervix | CC | Influenza A | 43/1267 | 171/8465 | 3.03e-04 | 1.64e-03 | 9.68e-04 | 43 |
hsa05171110 | Cervix | CC | Coronavirus disease - COVID-19 | 111/1267 | 232/8465 | 1.82e-33 | 5.90e-31 | 3.49e-31 | 111 |
hsa05169110 | Cervix | CC | Epstein-Barr virus infection | 57/1267 | 202/8465 | 7.30e-07 | 7.39e-06 | 4.37e-06 | 57 |
hsa0516415 | Cervix | CC | Influenza A | 43/1267 | 171/8465 | 3.03e-04 | 1.64e-03 | 9.68e-04 | 43 |
hsa05171 | Colorectum | AD | Coronavirus disease - COVID-19 | 113/2092 | 232/8465 | 9.90e-16 | 2.55e-14 | 1.63e-14 | 113 |
hsa05160 | Colorectum | AD | Hepatitis C | 54/2092 | 157/8465 | 3.87e-03 | 1.96e-02 | 1.25e-02 | 54 |
hsa051711 | Colorectum | AD | Coronavirus disease - COVID-19 | 113/2092 | 232/8465 | 9.90e-16 | 2.55e-14 | 1.63e-14 | 113 |
hsa051601 | Colorectum | AD | Hepatitis C | 54/2092 | 157/8465 | 3.87e-03 | 1.96e-02 | 1.25e-02 | 54 |
hsa051714 | Colorectum | MSS | Coronavirus disease - COVID-19 | 108/1875 | 232/8465 | 6.50e-17 | 1.67e-15 | 1.03e-15 | 108 |
hsa051602 | Colorectum | MSS | Hepatitis C | 52/1875 | 157/8465 | 9.29e-04 | 5.58e-03 | 3.42e-03 | 52 |
hsa05169 | Colorectum | MSS | Epstein-Barr virus infection | 63/1875 | 202/8465 | 1.63e-03 | 8.98e-03 | 5.50e-03 | 63 |
hsa05161 | Colorectum | MSS | Hepatitis B | 48/1875 | 162/8465 | 1.53e-02 | 4.93e-02 | 3.02e-02 | 48 |
hsa051715 | Colorectum | MSS | Coronavirus disease - COVID-19 | 108/1875 | 232/8465 | 6.50e-17 | 1.67e-15 | 1.03e-15 | 108 |
hsa051603 | Colorectum | MSS | Hepatitis C | 52/1875 | 157/8465 | 9.29e-04 | 5.58e-03 | 3.42e-03 | 52 |
hsa051691 | Colorectum | MSS | Epstein-Barr virus infection | 63/1875 | 202/8465 | 1.63e-03 | 8.98e-03 | 5.50e-03 | 63 |
hsa051611 | Colorectum | MSS | Hepatitis B | 48/1875 | 162/8465 | 1.53e-02 | 4.93e-02 | 3.02e-02 | 48 |
hsa051716 | Colorectum | MSI-H | Coronavirus disease - COVID-19 | 91/797 | 232/8465 | 2.21e-35 | 3.58e-33 | 3.00e-33 | 91 |
hsa051717 | Colorectum | MSI-H | Coronavirus disease - COVID-19 | 91/797 | 232/8465 | 2.21e-35 | 3.58e-33 | 3.00e-33 | 91 |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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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. |
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Somatic mutation of malignant transformation related genes |
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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 |
DDX58 | SNV | Missense_Mutation | rs759405155 | c.1076N>T | p.Thr359Met | p.T359M | O95786 | protein_coding | deleterious(0.03) | possibly_damaging(0.835) | TCGA-CM-6171-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
DDX58 | SNV | Missense_Mutation | c.2698N>A | p.Gly900Arg | p.G900R | O95786 | protein_coding | tolerated(0.07) | benign(0.051) | TCGA-D5-5539-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5-fu | PD | |
DDX58 | SNV | Missense_Mutation | c.452N>A | p.Gly151Asp | p.G151D | O95786 | protein_coding | deleterious(0) | probably_damaging(0.974) | TCGA-G4-6304-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Chemotherapy | fluorouracil | PD | |
DDX58 | SNV | Missense_Mutation | novel | c.2519N>G | p.Glu840Gly | p.E840G | O95786 | protein_coding | deleterious(0.02) | possibly_damaging(0.58) | TCGA-G4-6320-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | oxaliplatin | SD |
DDX58 | SNV | Missense_Mutation | c.148N>A | p.Pro50Thr | p.P50T | O95786 | protein_coding | tolerated(0.36) | benign(0.003) | TCGA-G4-6320-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | oxaliplatin | SD | |
DDX58 | SNV | Missense_Mutation | novel | c.1676N>A | p.Arg559Gln | p.R559Q | O95786 | protein_coding | tolerated(0.19) | benign(0.22) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
DDX58 | SNV | Missense_Mutation | rs749687427 | c.364N>A | p.Asp122Asn | p.D122N | O95786 | protein_coding | tolerated(0.06) | benign(0.227) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
DDX58 | SNV | Missense_Mutation | c.268N>A | p.Glu90Lys | p.E90K | O95786 | protein_coding | tolerated(0.17) | benign(0.02) | TCGA-CI-6622-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | I/II | Chemotherapy | 5-fluorouracil | SD | |
DDX58 | deletion | Frame_Shift_Del | c.2388delN | p.Lys796AsnfsTer28 | p.K796Nfs*28 | O95786 | protein_coding | TCGA-A6-3809-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |||
DDX58 | deletion | In_Frame_Del | c.1972_1983delCCTGGCATATTG | p.Pro658_Leu661del | p.P658_L661del | O95786 | protein_coding | TCGA-AA-A022-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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