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Gene: TRAPPC3 |
Gene summary for TRAPPC3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TRAPPC3 | Gene ID | 27095 |
| Gene name | trafficking protein particle complex subunit 3 | |
| Gene Alias | BET3 | |
| Cytomap | 1p34.3 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | A0A087WWM0 |
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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 |
| 27095 | TRAPPC3 | LZE2T | Human | Esophagus | ESCC | 9.96e-10 | 8.44e-01 | 0.082 |
| 27095 | TRAPPC3 | LZE3D | Human | Esophagus | HGIN | 1.66e-04 | 7.36e-01 | 0.0668 |
| 27095 | TRAPPC3 | LZE4T | Human | Esophagus | ESCC | 2.84e-15 | 4.25e-01 | 0.0811 |
| 27095 | TRAPPC3 | LZE5T | Human | Esophagus | ESCC | 4.96e-03 | 4.18e-01 | 0.0514 |
| 27095 | TRAPPC3 | LZE7T | Human | Esophagus | ESCC | 4.51e-08 | 7.02e-01 | 0.0667 |
| 27095 | TRAPPC3 | LZE8T | Human | Esophagus | ESCC | 5.34e-10 | 4.12e-01 | 0.067 |
| 27095 | TRAPPC3 | LZE20T | Human | Esophagus | ESCC | 4.52e-07 | 4.52e-01 | 0.0662 |
| 27095 | TRAPPC3 | LZE22D1 | Human | Esophagus | HGIN | 1.78e-04 | 2.20e-01 | 0.0595 |
| 27095 | TRAPPC3 | LZE22T | Human | Esophagus | ESCC | 3.96e-08 | 9.41e-01 | 0.068 |
| 27095 | TRAPPC3 | LZE24T | Human | Esophagus | ESCC | 8.80e-32 | 9.85e-01 | 0.0596 |
| 27095 | TRAPPC3 | LZE6T | Human | Esophagus | ESCC | 7.33e-06 | 5.73e-01 | 0.0845 |
| 27095 | TRAPPC3 | P1T-E | Human | Esophagus | ESCC | 6.74e-08 | 6.97e-01 | 0.0875 |
| 27095 | TRAPPC3 | P2T-E | Human | Esophagus | ESCC | 1.70e-50 | 1.07e+00 | 0.1177 |
| 27095 | TRAPPC3 | P4T-E | Human | Esophagus | ESCC | 1.58e-44 | 1.12e+00 | 0.1323 |
| 27095 | TRAPPC3 | P5T-E | Human | Esophagus | ESCC | 1.96e-44 | 9.42e-01 | 0.1327 |
| 27095 | TRAPPC3 | P8T-E | Human | Esophagus | ESCC | 2.04e-30 | 6.57e-01 | 0.0889 |
| 27095 | TRAPPC3 | P9T-E | Human | Esophagus | ESCC | 4.22e-23 | 6.06e-01 | 0.1131 |
| 27095 | TRAPPC3 | P10T-E | Human | Esophagus | ESCC | 1.20e-51 | 9.59e-01 | 0.116 |
| 27095 | TRAPPC3 | P11T-E | Human | Esophagus | ESCC | 2.30e-22 | 1.02e+00 | 0.1426 |
| 27095 | TRAPPC3 | P12T-E | Human | Esophagus | ESCC | 3.04e-34 | 7.75e-01 | 0.1122 |
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| 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:004819317 | Esophagus | HGIN | Golgi vesicle transport | 83/2587 | 296/18723 | 8.59e-11 | 8.89e-09 | 83 |
| GO:00068889 | Esophagus | HGIN | endoplasmic reticulum to Golgi vesicle-mediated transport | 40/2587 | 130/18723 | 4.67e-07 | 2.07e-05 | 40 |
| GO:004819318 | Esophagus | ESCC | Golgi vesicle transport | 231/8552 | 296/18723 | 1.82e-30 | 9.63e-28 | 231 |
| GO:000688815 | Esophagus | ESCC | endoplasmic reticulum to Golgi vesicle-mediated transport | 102/8552 | 130/18723 | 1.73e-14 | 9.22e-13 | 102 |
| GO:00068914 | Esophagus | ESCC | intra-Golgi vesicle-mediated transport | 26/8552 | 33/18723 | 1.06e-04 | 7.43e-04 | 26 |
| GO:004819311 | Liver | Cirrhotic | Golgi vesicle transport | 153/4634 | 296/18723 | 1.02e-23 | 6.43e-21 | 153 |
| GO:000688811 | Liver | Cirrhotic | endoplasmic reticulum to Golgi vesicle-mediated transport | 77/4634 | 130/18723 | 5.78e-17 | 7.56e-15 | 77 |
| GO:004819321 | Liver | HCC | Golgi vesicle transport | 217/7958 | 296/18723 | 2.58e-27 | 1.02e-24 | 217 |
| GO:000688821 | Liver | HCC | endoplasmic reticulum to Golgi vesicle-mediated transport | 100/7958 | 130/18723 | 1.15e-15 | 8.67e-14 | 100 |
| GO:0006891 | Liver | HCC | intra-Golgi vesicle-mediated transport | 22/7958 | 33/18723 | 4.38e-03 | 1.90e-02 | 22 |
| GO:004819315 | Oral cavity | OSCC | Golgi vesicle transport | 209/7305 | 296/18723 | 1.39e-28 | 6.30e-26 | 209 |
| GO:00068888 | Oral cavity | OSCC | endoplasmic reticulum to Golgi vesicle-mediated transport | 97/7305 | 130/18723 | 1.42e-16 | 1.15e-14 | 97 |
| GO:00068913 | Oral cavity | OSCC | intra-Golgi vesicle-mediated transport | 23/7305 | 33/18723 | 3.47e-04 | 2.12e-03 | 23 |
| GO:004819316 | Oral cavity | LP | Golgi vesicle transport | 141/4623 | 296/18723 | 6.11e-18 | 1.06e-15 | 141 |
| GO:000688814 | Oral cavity | LP | endoplasmic reticulum to Golgi vesicle-mediated transport | 67/4623 | 130/18723 | 3.74e-11 | 2.39e-09 | 67 |
| GO:000689111 | Oral cavity | LP | intra-Golgi vesicle-mediated transport | 16/4623 | 33/18723 | 2.59e-03 | 1.83e-02 | 16 |
| GO:0048193110 | Skin | cSCC | Golgi vesicle transport | 153/4864 | 296/18723 | 1.85e-21 | 3.41e-19 | 153 |
| GO:000688810 | Skin | cSCC | endoplasmic reticulum to Golgi vesicle-mediated transport | 73/4864 | 130/18723 | 2.60e-13 | 1.57e-11 | 73 |
| GO:000689112 | Skin | cSCC | intra-Golgi vesicle-mediated transport | 18/4864 | 33/18723 | 4.45e-04 | 3.42e-03 | 18 |
| GO:004819320 | Thyroid | PTC | Golgi vesicle transport | 186/5968 | 296/18723 | 3.09e-28 | 1.22e-25 | 186 |
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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 |
| TRAPPC3 | SNV | Missense_Mutation | c.52N>T | p.Leu18Phe | p.L18F | protein_coding | tolerated(0.07) | probably_damaging(0.91) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | ||
| TRAPPC3 | SNV | Missense_Mutation | c.190A>G | p.Ile64Val | p.I64V | protein_coding | tolerated(0.28) | benign(0.003) | TCGA-AD-5900-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | ||
| TRAPPC3 | SNV | Missense_Mutation | c.430C>T | p.Arg144Trp | p.R144W | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | ||
| TRAPPC3 | SNV | Missense_Mutation | novel | c.303T>G | p.Ile101Met | p.I101M | protein_coding | deleterious(0.02) | possibly_damaging(0.503) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| TRAPPC3 | insertion | Frame_Shift_Ins | novel | c.448_449insC | p.Val150AlafsTer31 | p.V150Afs*31 | protein_coding | TCGA-AM-5820-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |||
| TRAPPC3 | insertion | Frame_Shift_Ins | novel | c.448-1_448insT | p.Val150CysfsTer31 | p.V150Cfs*31 | protein_coding | TCGA-AM-5820-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |||
| TRAPPC3 | SNV | Missense_Mutation | novel | c.276N>T | p.Lys92Asn | p.K92N | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| TRAPPC3 | SNV | Missense_Mutation | novel | c.259N>A | p.Ala87Thr | p.A87T | protein_coding | deleterious(0.03) | probably_damaging(0.963) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TRAPPC3 | SNV | Missense_Mutation | novel | c.161C>A | p.Pro54His | p.P54H | protein_coding | tolerated_low_confidence(0.61) | benign(0) | TCGA-BS-A0UM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| TRAPPC3 | SNV | Missense_Mutation | c.42N>A | p.Met14Ile | p.M14I | protein_coding | tolerated(0.82) | benign(0.006) | TCGA-DD-A114-01 | Liver | liver hepatocellular carcinoma | Male | <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 |
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