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Gene: TRAPPC1 |
Gene summary for TRAPPC1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TRAPPC1 | Gene ID | 58485 |
| Gene name | trafficking protein particle complex subunit 1 | |
| Gene Alias | BET5 | |
| Cytomap | 17p13.1 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | Q9Y5R8 |
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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 |
| 58485 | TRAPPC1 | HTA11_866_3004761011 | Human | Colorectum | AD | 6.72e-05 | 1.97e-01 | 0.096 |
| 58485 | TRAPPC1 | HTA11_8622_2000001021 | Human | Colorectum | SER | 2.66e-03 | 2.73e-01 | 0.0528 |
| 58485 | TRAPPC1 | HTA11_10623_2000001011 | Human | Colorectum | AD | 3.41e-03 | 3.38e-01 | -0.0177 |
| 58485 | TRAPPC1 | HTA11_10711_2000001011 | Human | Colorectum | AD | 4.99e-05 | 2.70e-01 | 0.0338 |
| 58485 | TRAPPC1 | HTA11_7696_3000711011 | Human | Colorectum | AD | 8.47e-13 | 2.94e-01 | 0.0674 |
| 58485 | TRAPPC1 | HTA11_7469_2000001011 | Human | Colorectum | AD | 1.27e-02 | 4.40e-01 | -0.0124 |
| 58485 | TRAPPC1 | HTA11_6818_2000001021 | Human | Colorectum | AD | 8.07e-04 | 3.07e-01 | 0.0588 |
| 58485 | TRAPPC1 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 2.01e-06 | 1.83e-01 | 0.294 |
| 58485 | TRAPPC1 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 2.01e-06 | 7.08e-01 | 0.3487 |
| 58485 | TRAPPC1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 5.14e-07 | 2.19e-01 | 0.3859 |
| 58485 | TRAPPC1 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 3.05e-03 | 2.40e-01 | 0.2585 |
| 58485 | TRAPPC1 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 3.59e-14 | 2.85e-01 | 0.3005 |
| 58485 | TRAPPC1 | AEH-subject1 | Human | Endometrium | AEH | 7.00e-15 | -4.15e-01 | -0.3059 |
| 58485 | TRAPPC1 | AEH-subject2 | Human | Endometrium | AEH | 4.49e-10 | -4.20e-01 | -0.2525 |
| 58485 | TRAPPC1 | AEH-subject3 | Human | Endometrium | AEH | 3.18e-10 | -3.67e-01 | -0.2576 |
| 58485 | TRAPPC1 | AEH-subject4 | Human | Endometrium | AEH | 4.00e-08 | -4.08e-01 | -0.2657 |
| 58485 | TRAPPC1 | AEH-subject5 | Human | Endometrium | AEH | 8.63e-08 | -3.98e-01 | -0.2953 |
| 58485 | TRAPPC1 | EEC-subject1 | Human | Endometrium | EEC | 1.63e-18 | -4.27e-01 | -0.2682 |
| 58485 | TRAPPC1 | EEC-subject2 | Human | Endometrium | EEC | 2.97e-18 | -4.91e-01 | -0.2607 |
| 58485 | TRAPPC1 | EEC-subject3 | Human | Endometrium | EEC | 9.31e-47 | -5.33e-01 | -0.2525 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| 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:190382910 | Cervix | CC | positive regulation of cellular protein localization | 72/2311 | 276/18723 | 3.20e-10 | 4.46e-08 | 72 |
| GO:004325410 | Cervix | CC | regulation of protein-containing complex assembly | 96/2311 | 428/18723 | 2.91e-09 | 3.05e-07 | 96 |
| GO:00516567 | Cervix | CC | establishment of organelle localization | 76/2311 | 390/18723 | 3.17e-05 | 5.21e-04 | 76 |
| GO:00161977 | Cervix | CC | endosomal transport | 48/2311 | 230/18723 | 1.65e-04 | 1.97e-03 | 48 |
| GO:00481938 | Cervix | CC | Golgi vesicle transport | 58/2311 | 296/18723 | 2.24e-04 | 2.54e-03 | 58 |
| GO:19021153 | Cervix | CC | regulation of organelle assembly | 40/2311 | 186/18723 | 2.92e-04 | 3.15e-03 | 40 |
| GO:00070304 | Cervix | CC | Golgi organization | 32/2311 | 157/18723 | 2.78e-03 | 1.87e-02 | 32 |
| GO:00164827 | Cervix | CC | cytosolic transport | 33/2311 | 168/18723 | 4.43e-03 | 2.70e-02 | 33 |
| 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:00481931 | Colorectum | SER | Golgi vesicle transport | 79/2897 | 296/18723 | 4.20e-07 | 2.15e-05 | 79 |
| 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:00068883 | Colorectum | MSI-H | endoplasmic reticulum to Golgi vesicle-mediated transport | 22/1319 | 130/18723 | 1.05e-04 | 3.24e-03 | 22 |
| GO:00481933 | Colorectum | MSI-H | Golgi vesicle transport | 39/1319 | 296/18723 | 1.17e-04 | 3.51e-03 | 39 |
| GO:00481939 | Endometrium | AEH | Golgi vesicle transport | 60/2100 | 296/18723 | 3.65e-06 | 9.79e-05 | 60 |
| GO:00068886 | Endometrium | AEH | endoplasmic reticulum to Golgi vesicle-mediated transport | 29/2100 | 130/18723 | 2.11e-04 | 2.59e-03 | 29 |
| GO:004819313 | Endometrium | EEC | Golgi vesicle transport | 60/2168 | 296/18723 | 9.91e-06 | 2.17e-04 | 60 |
| GO:000688812 | Endometrium | EEC | endoplasmic reticulum to Golgi vesicle-mediated transport | 29/2168 | 130/18723 | 3.63e-04 | 3.95e-03 | 29 |
| Page: 1 2 3 4 5 6 7 8 |
| 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 |
| TRAPPC1 | SNV | Missense_Mutation | c.140N>G | p.Ser47Trp | p.S47W | Q9Y5R8 | protein_coding | deleterious(0) | probably_damaging(0.993) | TCGA-AN-A0XW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| TRAPPC1 | SNV | Missense_Mutation | c.386N>A | p.Arg129Gln | p.R129Q | Q9Y5R8 | protein_coding | tolerated(0.26) | benign(0.003) | TCGA-AQ-A1H2-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | herceptin | SD | |
| TRAPPC1 | SNV | Missense_Mutation | rs148790381 | c.379N>T | p.Arg127Cys | p.R127C | Q9Y5R8 | protein_coding | deleterious(0.05) | possibly_damaging(0.74) | TCGA-EA-A3HS-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| TRAPPC1 | SNV | Missense_Mutation | c.427N>T | p.Arg143Trp | p.R143W | Q9Y5R8 | protein_coding | deleterious(0) | possibly_damaging(0.798) | TCGA-AZ-6598-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TRAPPC1 | SNV | Missense_Mutation | c.5N>T | p.Thr2Ile | p.T2I | Q9Y5R8 | protein_coding | deleterious(0.01) | probably_damaging(0.934) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TRAPPC1 | SNV | Missense_Mutation | novel | c.68N>A | p.Arg23His | p.R23H | Q9Y5R8 | protein_coding | deleterious(0) | possibly_damaging(0.486) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TRAPPC1 | SNV | Missense_Mutation | c.314A>G | p.Tyr105Cys | p.Y105C | Q9Y5R8 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-B5-A0JY-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD | |
| TRAPPC1 | SNV | Missense_Mutation | c.72N>T | p.Lys24Asn | p.K24N | Q9Y5R8 | protein_coding | tolerated(0.5) | benign(0.153) | TCGA-BS-A0UF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TRAPPC1 | SNV | Missense_Mutation | c.227C>T | p.Thr76Met | p.T76M | Q9Y5R8 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-97-8171-01 | Lung | lung adenocarcinoma | Male | >=65 | III/IV | Targeted Molecular therapy | tarceva | PD | |
| TRAPPC1 | SNV | Missense_Mutation | c.347N>T | p.Pro116Leu | p.P116L | Q9Y5R8 | protein_coding | tolerated(0.27) | benign(0.052) | TCGA-BR-8078-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 |
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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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