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Gene: THUMPD1 |
Gene summary for THUMPD1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | THUMPD1 | Gene ID | 55623 |
| Gene name | THUMP domain containing 1 | |
| Gene Alias | Tan1 | |
| Cytomap | 16p12.3 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | A0A024R388 |
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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 |
| 55623 | THUMPD1 | LZE4T | Human | Esophagus | ESCC | 1.02e-11 | 2.42e-01 | 0.0811 |
| 55623 | THUMPD1 | LZE5T | Human | Esophagus | ESCC | 9.95e-07 | 3.76e-01 | 0.0514 |
| 55623 | THUMPD1 | LZE7T | Human | Esophagus | ESCC | 9.30e-06 | 2.77e-01 | 0.0667 |
| 55623 | THUMPD1 | LZE8T | Human | Esophagus | ESCC | 1.55e-06 | 1.78e-01 | 0.067 |
| 55623 | THUMPD1 | LZE20T | Human | Esophagus | ESCC | 7.91e-06 | 1.63e-01 | 0.0662 |
| 55623 | THUMPD1 | LZE24T | Human | Esophagus | ESCC | 6.54e-15 | 2.88e-01 | 0.0596 |
| 55623 | THUMPD1 | LZE21T | Human | Esophagus | ESCC | 1.54e-02 | 2.06e-01 | 0.0655 |
| 55623 | THUMPD1 | LZE6T | Human | Esophagus | ESCC | 4.77e-04 | 1.28e-01 | 0.0845 |
| 55623 | THUMPD1 | P1T-E | Human | Esophagus | ESCC | 1.16e-02 | 2.93e-01 | 0.0875 |
| 55623 | THUMPD1 | P2T-E | Human | Esophagus | ESCC | 2.11e-55 | 1.04e+00 | 0.1177 |
| 55623 | THUMPD1 | P4T-E | Human | Esophagus | ESCC | 1.04e-18 | 4.16e-01 | 0.1323 |
| 55623 | THUMPD1 | P5T-E | Human | Esophagus | ESCC | 4.15e-05 | 2.21e-01 | 0.1327 |
| 55623 | THUMPD1 | P8T-E | Human | Esophagus | ESCC | 7.74e-26 | 4.66e-01 | 0.0889 |
| 55623 | THUMPD1 | P9T-E | Human | Esophagus | ESCC | 4.33e-06 | 1.33e-01 | 0.1131 |
| 55623 | THUMPD1 | P10T-E | Human | Esophagus | ESCC | 4.54e-14 | 3.57e-01 | 0.116 |
| 55623 | THUMPD1 | P11T-E | Human | Esophagus | ESCC | 4.79e-17 | 7.17e-01 | 0.1426 |
| 55623 | THUMPD1 | P12T-E | Human | Esophagus | ESCC | 1.03e-45 | 8.56e-01 | 0.1122 |
| 55623 | THUMPD1 | P15T-E | Human | Esophagus | ESCC | 1.84e-20 | 4.36e-01 | 0.1149 |
| 55623 | THUMPD1 | P16T-E | Human | Esophagus | ESCC | 6.86e-37 | 7.65e-01 | 0.1153 |
| 55623 | THUMPD1 | P17T-E | Human | Esophagus | ESCC | 8.02e-07 | 4.34e-01 | 0.1278 |
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:003447015 | Esophagus | ESCC | ncRNA processing | 300/8552 | 395/18723 | 3.09e-35 | 3.26e-32 | 300 |
| GO:003466012 | Esophagus | ESCC | ncRNA metabolic process | 346/8552 | 485/18723 | 4.35e-31 | 2.51e-28 | 346 |
| GO:00080333 | Esophagus | ESCC | tRNA processing | 92/8552 | 127/18723 | 7.83e-10 | 1.93e-08 | 92 |
| GO:00063992 | Esophagus | ESCC | tRNA metabolic process | 122/8552 | 179/18723 | 9.03e-10 | 2.19e-08 | 122 |
| GO:00094512 | Esophagus | ESCC | RNA modification | 114/8552 | 167/18723 | 2.76e-09 | 6.04e-08 | 114 |
| GO:00064002 | Esophagus | ESCC | tRNA modification | 62/8552 | 90/18723 | 7.02e-06 | 7.04e-05 | 62 |
| 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:00344702 | Liver | HCC | ncRNA processing | 293/7958 | 395/18723 | 4.26e-38 | 6.76e-35 | 293 |
| GO:00346601 | Liver | HCC | ncRNA metabolic process | 332/7958 | 485/18723 | 1.48e-31 | 7.80e-29 | 332 |
| GO:0008033 | Liver | HCC | tRNA processing | 87/7958 | 127/18723 | 2.66e-09 | 7.23e-08 | 87 |
| GO:0006399 | Liver | HCC | tRNA metabolic process | 108/7958 | 179/18723 | 1.07e-06 | 1.59e-05 | 108 |
| GO:0009451 | Liver | HCC | RNA modification | 101/7958 | 167/18723 | 2.02e-06 | 2.78e-05 | 101 |
| GO:0006400 | Liver | HCC | tRNA modification | 60/7958 | 90/18723 | 3.09e-06 | 4.09e-05 | 60 |
| GO:00344709 | Oral cavity | OSCC | ncRNA processing | 263/7305 | 395/18723 | 4.38e-29 | 2.78e-26 | 263 |
| GO:00346605 | Oral cavity | OSCC | ncRNA metabolic process | 296/7305 | 485/18723 | 2.94e-23 | 6.65e-21 | 296 |
| GO:00080332 | Oral cavity | OSCC | tRNA processing | 78/7305 | 127/18723 | 2.56e-07 | 4.00e-06 | 78 |
| GO:00063991 | Oral cavity | OSCC | tRNA metabolic process | 101/7305 | 179/18723 | 1.65e-06 | 2.15e-05 | 101 |
| GO:00094511 | Oral cavity | OSCC | RNA modification | 95/7305 | 167/18723 | 2.05e-06 | 2.62e-05 | 95 |
| GO:00064001 | Oral cavity | OSCC | tRNA modification | 53/7305 | 90/18723 | 1.04e-04 | 7.70e-04 | 53 |
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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 |
| THUMPD1 | SNV | Missense_Mutation | rs764908847 | c.608G>A | p.Arg203Gln | p.R203Q | Q9NXG2 | protein_coding | tolerated(0.08) | possibly_damaging(0.57) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| THUMPD1 | SNV | Missense_Mutation | c.445N>C | p.Tyr149His | p.Y149H | Q9NXG2 | protein_coding | tolerated(0.68) | benign(0.003) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| THUMPD1 | SNV | Missense_Mutation | rs368837394 | c.14N>T | p.Ala5Val | p.A5V | Q9NXG2 | protein_coding | tolerated_low_confidence(0.87) | benign(0) | TCGA-AG-3732-01 | Colorectum | rectum adenocarcinoma | Female | >=65 | I/II | Chemotherapy | capecitabine | SD |
| THUMPD1 | SNV | Missense_Mutation | novel | c.344N>T | p.Arg115Ile | p.R115I | Q9NXG2 | protein_coding | deleterious(0) | probably_damaging(0.956) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| THUMPD1 | insertion | Frame_Shift_Ins | novel | c.534_535insA | p.Tyr179IlefsTer11 | p.Y179Ifs*11 | Q9NXG2 | protein_coding | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | ||
| THUMPD1 | SNV | Missense_Mutation | c.905N>T | p.Glu302Val | p.E302V | Q9NXG2 | protein_coding | deleterious(0.01) | benign(0.178) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| THUMPD1 | SNV | Missense_Mutation | novel | c.146C>A | p.Thr49Asn | p.T49N | Q9NXG2 | protein_coding | deleterious(0) | possibly_damaging(0.843) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| THUMPD1 | SNV | Missense_Mutation | c.387C>A | p.Phe129Leu | p.F129L | Q9NXG2 | protein_coding | deleterious(0) | possibly_damaging(0.527) | TCGA-AX-A0J0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| THUMPD1 | SNV | Missense_Mutation | novel | c.625N>C | p.Asn209His | p.N209H | Q9NXG2 | protein_coding | tolerated(0.15) | probably_damaging(0.913) | TCGA-AX-A2HC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | PD |
| THUMPD1 | SNV | Missense_Mutation | rs764908847 | c.608N>A | p.Arg203Gln | p.R203Q | Q9NXG2 | protein_coding | tolerated(0.08) | possibly_damaging(0.57) | TCGA-B5-A1MR-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | 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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