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Gene: PAPD4 |
Gene summary for PAPD4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PAPD4 | Gene ID | 167153 |
| Gene name | terminal nucleotidyltransferase 2 | |
| Gene Alias | APD4 | |
| Cytomap | 5q14.1 | |
| Gene Type | protein-coding | GO ID | GO:0000956 | UniProtAcc | Q6PIY7 |
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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 |
| 167153 | PAPD4 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.29e-28 | 5.11e-01 | 0.294 |
| 167153 | PAPD4 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 5.11e-13 | 1.04e+00 | 0.3487 |
| 167153 | PAPD4 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 2.80e-21 | 6.80e-01 | 0.281 |
| 167153 | PAPD4 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 1.29e-28 | 5.97e-01 | 0.3859 |
| 167153 | PAPD4 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 5.79e-04 | 2.27e-01 | 0.2585 |
| 167153 | PAPD4 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.73e-12 | 2.44e-01 | 0.3005 |
| 167153 | PAPD4 | P1T-E | Human | Esophagus | ESCC | 3.10e-03 | 9.26e-02 | 0.0875 |
| 167153 | PAPD4 | P2T-E | Human | Esophagus | ESCC | 1.09e-17 | 3.38e-01 | 0.1177 |
| 167153 | PAPD4 | P4T-E | Human | Esophagus | ESCC | 1.35e-14 | 2.45e-01 | 0.1323 |
| 167153 | PAPD4 | P5T-E | Human | Esophagus | ESCC | 1.16e-11 | 1.10e-01 | 0.1327 |
| 167153 | PAPD4 | P8T-E | Human | Esophagus | ESCC | 1.38e-13 | 2.22e-01 | 0.0889 |
| 167153 | PAPD4 | P9T-E | Human | Esophagus | ESCC | 3.58e-10 | 1.73e-01 | 0.1131 |
| 167153 | PAPD4 | P10T-E | Human | Esophagus | ESCC | 1.01e-18 | 2.52e-01 | 0.116 |
| 167153 | PAPD4 | P11T-E | Human | Esophagus | ESCC | 1.30e-12 | 2.72e-01 | 0.1426 |
| 167153 | PAPD4 | P12T-E | Human | Esophagus | ESCC | 1.01e-19 | 3.44e-01 | 0.1122 |
| 167153 | PAPD4 | P15T-E | Human | Esophagus | ESCC | 6.04e-21 | 3.23e-01 | 0.1149 |
| 167153 | PAPD4 | P16T-E | Human | Esophagus | ESCC | 5.84e-21 | 2.35e-01 | 0.1153 |
| 167153 | PAPD4 | P17T-E | Human | Esophagus | ESCC | 8.99e-04 | 1.70e-01 | 0.1278 |
| 167153 | PAPD4 | P20T-E | Human | Esophagus | ESCC | 1.06e-16 | 3.83e-01 | 0.1124 |
| 167153 | PAPD4 | P21T-E | Human | Esophagus | ESCC | 8.24e-12 | 2.33e-01 | 0.1617 |
| Page: 1 2 3 4 5 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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. |
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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 |
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| 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 |
| PAPD4 | SNV | Missense_Mutation | novel | c.269N>T | p.Arg90Leu | p.R90L | Q6PIY7 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.98) | TCGA-86-7701-01 | Lung | lung adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | etoposide | PD |
| PAPD4 | SNV | Missense_Mutation | c.7N>G | p.Pro3Ala | p.P3A | Q6PIY7 | protein_coding | deleterious_low_confidence(0.02) | probably_damaging(0.991) | TCGA-95-7944-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| PAPD4 | SNV | Missense_Mutation | novel | c.916C>T | p.Pro306Ser | p.P306S | Q6PIY7 | protein_coding | deleterious(0) | probably_damaging(0.917) | TCGA-60-2703-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| PAPD4 | SNV | Missense_Mutation | novel | c.637N>A | p.Asp213Asn | p.D213N | Q6PIY7 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-CN-A6V1-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Immunotherapy | erbitux | CR |
| PAPD4 | SNV | Missense_Mutation | novel | c.1328N>A | p.Arg443Lys | p.R443K | Q6PIY7 | protein_coding | deleterious(0) | possibly_damaging(0.878) | TCGA-CV-7568-01 | Oral cavity | head & neck squamous cell carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PAPD4 | SNV | Missense_Mutation | c.238G>A | p.Asp80Asn | p.D80N | Q6PIY7 | protein_coding | tolerated(0.45) | benign(0) | TCGA-CV-A6JO-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| PAPD4 | SNV | Missense_Mutation | c.455N>T | p.Ala152Val | p.A152V | Q6PIY7 | protein_coding | tolerated(0.19) | benign(0.039) | TCGA-BR-7851-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| PAPD4 | SNV | Missense_Mutation | c.1392N>T | p.Arg464Ser | p.R464S | Q6PIY7 | protein_coding | tolerated(0.19) | benign(0.065) | TCGA-CG-4305-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Chemotherapy | cisplatin | CR | |
| PAPD4 | SNV | Missense_Mutation | c.1085C>T | p.Pro362Leu | p.P362L | Q6PIY7 | protein_coding | tolerated(0.11) | benign(0) | TCGA-HU-A4H3-01 | Stomach | stomach adenocarcinoma | Female | <65 | III/IV | Chemotherapy | ts-1 | PD | |
| PAPD4 | deletion | Frame_Shift_Del | novel | c.1417_1426delAGTATACTAC | p.Ser473LeufsTer2 | p.S473Lfs*2 | Q6PIY7 | protein_coding | TCGA-CG-5725-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Chemotherapy | docetaxel | PD |
| Page: 1 2 3 4 5 6 |
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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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