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Gene: DDX56 |
Gene summary for DDX56 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | DDX56 | Gene ID | 54606 |
| Gene name | DEAD-box helicase 56 | |
| Gene Alias | DDX21 | |
| Cytomap | 7p13 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | Q9NY93 |
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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 |
| 54606 | DDX56 | LZE2T | Human | Esophagus | ESCC | 7.45e-03 | 2.39e-01 | 0.082 |
| 54606 | DDX56 | LZE4T | Human | Esophagus | ESCC | 2.44e-08 | 3.09e-01 | 0.0811 |
| 54606 | DDX56 | LZE5T | Human | Esophagus | ESCC | 8.30e-05 | 3.42e-01 | 0.0514 |
| 54606 | DDX56 | LZE7T | Human | Esophagus | ESCC | 5.64e-11 | 5.62e-01 | 0.0667 |
| 54606 | DDX56 | LZE8T | Human | Esophagus | ESCC | 1.39e-09 | 2.63e-01 | 0.067 |
| 54606 | DDX56 | LZE22T | Human | Esophagus | ESCC | 2.12e-06 | 4.38e-01 | 0.068 |
| 54606 | DDX56 | LZE24T | Human | Esophagus | ESCC | 1.86e-20 | 5.36e-01 | 0.0596 |
| 54606 | DDX56 | LZE6T | Human | Esophagus | ESCC | 2.54e-09 | 3.80e-01 | 0.0845 |
| 54606 | DDX56 | P1T-E | Human | Esophagus | ESCC | 3.84e-14 | 4.90e-01 | 0.0875 |
| 54606 | DDX56 | P2T-E | Human | Esophagus | ESCC | 2.37e-29 | 5.18e-01 | 0.1177 |
| 54606 | DDX56 | P4T-E | Human | Esophagus | ESCC | 4.20e-25 | 6.45e-01 | 0.1323 |
| 54606 | DDX56 | P5T-E | Human | Esophagus | ESCC | 4.54e-13 | 1.73e-01 | 0.1327 |
| 54606 | DDX56 | P8T-E | Human | Esophagus | ESCC | 1.90e-25 | 3.86e-01 | 0.0889 |
| 54606 | DDX56 | P9T-E | Human | Esophagus | ESCC | 1.12e-17 | 4.24e-01 | 0.1131 |
| 54606 | DDX56 | P10T-E | Human | Esophagus | ESCC | 3.26e-31 | 5.51e-01 | 0.116 |
| 54606 | DDX56 | P11T-E | Human | Esophagus | ESCC | 2.78e-22 | 7.97e-01 | 0.1426 |
| 54606 | DDX56 | P12T-E | Human | Esophagus | ESCC | 2.63e-27 | 6.44e-01 | 0.1122 |
| 54606 | DDX56 | P15T-E | Human | Esophagus | ESCC | 4.09e-33 | 6.74e-01 | 0.1149 |
| 54606 | DDX56 | P16T-E | Human | Esophagus | ESCC | 9.83e-42 | 7.62e-01 | 0.1153 |
| 54606 | DDX56 | P17T-E | Human | Esophagus | ESCC | 1.36e-13 | 6.57e-01 | 0.1278 |
| 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 | ||
| 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:003134616 | Esophagus | ESCC | positive regulation of cell projection organization | 201/8552 | 353/18723 | 1.19e-05 | 1.11e-04 | 201 |
| GO:001097516 | Esophagus | ESCC | regulation of neuron projection development | 240/8552 | 445/18723 | 2.48e-04 | 1.53e-03 | 240 |
| GO:00109764 | Esophagus | ESCC | positive regulation of neuron projection development | 91/8552 | 163/18723 | 5.72e-03 | 2.13e-02 | 91 |
| GO:002261312 | Liver | Cirrhotic | ribonucleoprotein complex biogenesis | 231/4634 | 463/18723 | 3.28e-32 | 6.86e-29 | 231 |
| GO:004225412 | Liver | Cirrhotic | ribosome biogenesis | 154/4634 | 299/18723 | 1.18e-23 | 6.72e-21 | 154 |
| GO:000636412 | Liver | Cirrhotic | rRNA processing | 115/4634 | 225/18723 | 1.12e-17 | 1.64e-15 | 115 |
| GO:00160724 | Liver | Cirrhotic | rRNA metabolic process | 119/4634 | 236/18723 | 1.19e-17 | 1.70e-15 | 119 |
| GO:00344701 | Liver | Cirrhotic | ncRNA processing | 158/4634 | 395/18723 | 1.09e-11 | 6.96e-10 | 158 |
| GO:00346603 | Liver | Cirrhotic | ncRNA metabolic process | 173/4634 | 485/18723 | 3.64e-08 | 1.21e-06 | 173 |
| 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 |
| 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 |
| DDX56 | SNV | Missense_Mutation | rs144918436 | c.1115N>A | p.Arg372Gln | p.R372Q | Q9NY93 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-BR-8680-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatin | CR |
| DDX56 | SNV | Missense_Mutation | c.1403N>A | p.Pro468His | p.P468H | Q9NY93 | protein_coding | deleterious(0) | probably_damaging(0.993) | TCGA-CG-5721-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Unknown | Unknown | SD | |
| DDX56 | SNV | Missense_Mutation | novel | c.201N>T | p.Gln67His | p.Q67H | Q9NY93 | protein_coding | deleterious(0.05) | possibly_damaging(0.893) | TCGA-VQ-A8P2-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Unspecific | Complete Response | |
| DDX56 | SNV | Missense_Mutation | novel | c.23N>T | p.Gly8Val | p.G8V | Q9NY93 | protein_coding | tolerated(0.18) | benign(0.115) | TCGA-VQ-A8P2-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Unspecific | Complete Response | |
| DDX56 | SNV | Missense_Mutation | c.1115G>T | p.Arg372Leu | p.R372L | Q9NY93 | protein_coding | deleterious(0.02) | probably_damaging(0.99) | TCGA-VQ-A94U-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 |
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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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