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Gene: TRAPPC4 |
Gene summary for TRAPPC4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TRAPPC4 | Gene ID | 51399 |
| Gene name | trafficking protein particle complex subunit 4 | |
| Gene Alias | CGI-104 | |
| Cytomap | 11q23.3 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | Q9Y296 |
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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 |
| 51399 | TRAPPC4 | HTA11_347_2000001011 | Human | Colorectum | AD | 5.20e-03 | 1.56e-01 | -0.1954 |
| 51399 | TRAPPC4 | HTA11_411_2000001011 | Human | Colorectum | SER | 1.43e-06 | 6.43e-01 | -0.2602 |
| 51399 | TRAPPC4 | HTA11_866_3004761011 | Human | Colorectum | AD | 8.32e-03 | 1.91e-01 | 0.096 |
| 51399 | TRAPPC4 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.24e-04 | 2.76e-01 | 0.294 |
| 51399 | TRAPPC4 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 4.22e-09 | 3.69e-01 | 0.3859 |
| 51399 | TRAPPC4 | LZE4T | Human | Esophagus | ESCC | 1.74e-15 | 4.14e-01 | 0.0811 |
| 51399 | TRAPPC4 | LZE8T | Human | Esophagus | ESCC | 2.46e-07 | 1.43e-01 | 0.067 |
| 51399 | TRAPPC4 | LZE20T | Human | Esophagus | ESCC | 4.02e-03 | 2.10e-01 | 0.0662 |
| 51399 | TRAPPC4 | LZE22D1 | Human | Esophagus | HGIN | 1.70e-07 | 4.46e-01 | 0.0595 |
| 51399 | TRAPPC4 | LZE22T | Human | Esophagus | ESCC | 2.13e-14 | 1.59e+00 | 0.068 |
| 51399 | TRAPPC4 | LZE24T | Human | Esophagus | ESCC | 4.64e-17 | 6.83e-01 | 0.0596 |
| 51399 | TRAPPC4 | P1T-E | Human | Esophagus | ESCC | 1.96e-04 | 2.50e-01 | 0.0875 |
| 51399 | TRAPPC4 | P2T-E | Human | Esophagus | ESCC | 6.75e-26 | 3.40e-01 | 0.1177 |
| 51399 | TRAPPC4 | P4T-E | Human | Esophagus | ESCC | 9.32e-56 | 1.48e+00 | 0.1323 |
| 51399 | TRAPPC4 | P5T-E | Human | Esophagus | ESCC | 3.86e-34 | 5.99e-01 | 0.1327 |
| 51399 | TRAPPC4 | P8T-E | Human | Esophagus | ESCC | 4.71e-15 | 3.64e-01 | 0.0889 |
| 51399 | TRAPPC4 | P9T-E | Human | Esophagus | ESCC | 1.53e-18 | 4.50e-01 | 0.1131 |
| 51399 | TRAPPC4 | P10T-E | Human | Esophagus | ESCC | 1.55e-25 | 4.11e-01 | 0.116 |
| 51399 | TRAPPC4 | P11T-E | Human | Esophagus | ESCC | 6.66e-15 | 8.33e-01 | 0.1426 |
| 51399 | TRAPPC4 | P12T-E | Human | Esophagus | ESCC | 2.06e-45 | 7.51e-01 | 0.1122 |
| Page: 1 2 3 4 5 6 7 |
| 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 | ||
| 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:0048193 | Colorectum | AD | Golgi vesicle transport | 109/3918 | 296/18723 | 1.80e-10 | 1.68e-08 | 109 |
| GO:0006888 | Colorectum | AD | endoplasmic reticulum to Golgi vesicle-mediated transport | 44/3918 | 130/18723 | 4.13e-04 | 4.68e-03 | 44 |
| GO:0016358 | Colorectum | AD | dendrite development | 69/3918 | 243/18723 | 3.32e-03 | 2.42e-02 | 69 |
| GO:00481931 | Colorectum | SER | Golgi vesicle transport | 79/2897 | 296/18723 | 4.20e-07 | 2.15e-05 | 79 |
| GO:00163581 | Colorectum | SER | dendrite development | 58/2897 | 243/18723 | 3.82e-04 | 5.81e-03 | 58 |
| GO:00068881 | Colorectum | SER | endoplasmic reticulum to Golgi vesicle-mediated transport | 34/2897 | 130/18723 | 1.13e-03 | 1.29e-02 | 34 |
| GO:00481932 | Colorectum | MSS | Golgi vesicle transport | 101/3467 | 296/18723 | 9.09e-11 | 9.77e-09 | 101 |
| GO:00068882 | Colorectum | MSS | endoplasmic reticulum to Golgi vesicle-mediated transport | 44/3467 | 130/18723 | 2.17e-05 | 4.60e-04 | 44 |
| GO:00163582 | Colorectum | MSS | dendrite development | 65/3467 | 243/18723 | 9.41e-04 | 9.50e-03 | 65 |
| 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:001635816 | Esophagus | ESCC | dendrite development | 130/8552 | 243/18723 | 8.33e-03 | 2.95e-02 | 130 |
| 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:001635811 | Liver | HCC | dendrite development | 121/7958 | 243/18723 | 1.26e-02 | 4.56e-02 | 121 |
| GO:004819315 | Oral cavity | OSCC | Golgi vesicle transport | 209/7305 | 296/18723 | 1.39e-28 | 6.30e-26 | 209 |
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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 |
| TRAPPC4 | SNV | Missense_Mutation | novel | c.630N>T | p.Glu210Asp | p.E210D | Q9Y296 | protein_coding | tolerated(0.16) | benign(0.021) | TCGA-IR-A3LK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD |
| TRAPPC4 | SNV | Missense_Mutation | novel | c.159G>C | p.Gln53His | p.Q53H | Q9Y296 | protein_coding | deleterious(0.01) | probably_damaging(0.915) | TCGA-VS-A8EJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
| TRAPPC4 | SNV | Missense_Mutation | c.149N>T | p.Ala50Val | p.A50V | Q9Y296 | protein_coding | tolerated(0.57) | benign(0.003) | TCGA-AA-3672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| TRAPPC4 | SNV | Missense_Mutation | c.528T>G | p.Ile176Met | p.I176M | Q9Y296 | protein_coding | deleterious(0.02) | benign(0.321) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| TRAPPC4 | SNV | Missense_Mutation | novel | c.280G>T | p.Val94Leu | p.V94L | Q9Y296 | protein_coding | tolerated(0.88) | benign(0.001) | TCGA-AG-A023-01 | Colorectum | rectum adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
| TRAPPC4 | insertion | Frame_Shift_Ins | novel | c.93_94insGGTA | p.Phe32GlyfsTer15 | p.F32Gfs*15 | Q9Y296 | protein_coding | TCGA-AM-5820-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| TRAPPC4 | SNV | Missense_Mutation | c.123G>T | p.Lys41Asn | p.K41N | Q9Y296 | protein_coding | tolerated(0.28) | benign(0.209) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD | |
| TRAPPC4 | SNV | Missense_Mutation | novel | c.92N>A | p.Thr31Asn | p.T31N | Q9Y296 | protein_coding | deleterious(0.01) | probably_damaging(0.921) | TCGA-AX-A2HC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | PD |
| TRAPPC4 | SNV | Missense_Mutation | novel | c.182N>G | p.His61Arg | p.H61R | Q9Y296 | protein_coding | deleterious(0.01) | benign(0.011) | TCGA-B5-A11E-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TRAPPC4 | SNV | Missense_Mutation | rs782598621 | c.512G>A | p.Arg171Gln | p.R171Q | Q9Y296 | protein_coding | deleterious(0.01) | benign(0.189) | 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 |
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