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Gene: TRAPPC8 |
Gene summary for TRAPPC8 |
Gene summary. |
Gene information | Species | Human | Gene symbol | TRAPPC8 | Gene ID | 22878 |
Gene name | trafficking protein particle complex subunit 8 | |
Gene Alias | GSG1 | |
Cytomap | 18q12.1 | |
Gene Type | protein-coding | GO ID | GO:0000045 | UniProtAcc | Q9Y2L5 |
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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 |
22878 | TRAPPC8 | CCI_2 | Human | Cervix | CC | 1.40e-04 | 6.89e-01 | 0.5249 |
22878 | TRAPPC8 | CCI_3 | Human | Cervix | CC | 2.38e-04 | 5.51e-01 | 0.516 |
22878 | TRAPPC8 | T3 | Human | Cervix | CC | 1.46e-02 | 7.74e-02 | 0.1389 |
22878 | TRAPPC8 | HTA11_3410_2000001011 | Human | Colorectum | AD | 8.99e-11 | -4.81e-01 | 0.0155 |
22878 | TRAPPC8 | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.08e-03 | -4.74e-01 | -0.1207 |
22878 | TRAPPC8 | HTA11_696_2000001011 | Human | Colorectum | AD | 2.76e-06 | -3.33e-01 | -0.1464 |
22878 | TRAPPC8 | HTA11_1391_2000001011 | Human | Colorectum | AD | 2.56e-02 | -3.11e-01 | -0.059 |
22878 | TRAPPC8 | HTA11_546_2000001011 | Human | Colorectum | AD | 1.40e-02 | -4.84e-01 | -0.0842 |
22878 | TRAPPC8 | HTA11_866_3004761011 | Human | Colorectum | AD | 1.55e-10 | -4.78e-01 | 0.096 |
22878 | TRAPPC8 | HTA11_10711_2000001011 | Human | Colorectum | AD | 7.07e-05 | -4.66e-01 | 0.0338 |
22878 | TRAPPC8 | HTA11_7696_3000711011 | Human | Colorectum | AD | 5.86e-08 | -4.25e-01 | 0.0674 |
22878 | TRAPPC8 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 6.17e-06 | -3.60e-01 | 0.294 |
22878 | TRAPPC8 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 1.55e-11 | -4.61e-01 | 0.3859 |
22878 | TRAPPC8 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 5.50e-17 | -5.41e-01 | 0.3005 |
22878 | TRAPPC8 | A002-C-010 | Human | Colorectum | FAP | 1.77e-02 | -1.43e-01 | 0.242 |
22878 | TRAPPC8 | A001-C-207 | Human | Colorectum | FAP | 6.02e-04 | -2.54e-01 | 0.1278 |
22878 | TRAPPC8 | A015-C-203 | Human | Colorectum | FAP | 6.09e-25 | -3.07e-01 | -0.1294 |
22878 | TRAPPC8 | A015-C-204 | Human | Colorectum | FAP | 5.65e-09 | -3.91e-01 | -0.0228 |
22878 | TRAPPC8 | A014-C-040 | Human | Colorectum | FAP | 1.05e-02 | -2.66e-01 | -0.1184 |
22878 | TRAPPC8 | A002-C-201 | Human | Colorectum | FAP | 1.64e-11 | -2.90e-01 | 0.0324 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00162367 | Cervix | CC | macroautophagy | 58/2311 | 291/18723 | 1.40e-04 | 1.70e-03 | 58 |
GO:00481938 | Cervix | CC | Golgi vesicle transport | 58/2311 | 296/18723 | 2.24e-04 | 2.54e-03 | 58 |
GO:00070304 | Cervix | CC | Golgi organization | 32/2311 | 157/18723 | 2.78e-03 | 1.87e-02 | 32 |
GO:00000452 | Cervix | CC | autophagosome assembly | 21/2311 | 99/18723 | 8.67e-03 | 4.46e-02 | 21 |
GO:0048193 | Colorectum | AD | Golgi vesicle transport | 109/3918 | 296/18723 | 1.80e-10 | 1.68e-08 | 109 |
GO:0016236 | Colorectum | AD | macroautophagy | 103/3918 | 291/18723 | 6.76e-09 | 4.15e-07 | 103 |
GO:0006888 | Colorectum | AD | endoplasmic reticulum to Golgi vesicle-mediated transport | 44/3918 | 130/18723 | 4.13e-04 | 4.68e-03 | 44 |
GO:0007033 | Colorectum | AD | vacuole organization | 53/3918 | 180/18723 | 4.18e-03 | 2.89e-02 | 53 |
GO:00481932 | Colorectum | MSS | Golgi vesicle transport | 101/3467 | 296/18723 | 9.09e-11 | 9.77e-09 | 101 |
GO:00162362 | Colorectum | MSS | macroautophagy | 93/3467 | 291/18723 | 2.08e-08 | 1.17e-06 | 93 |
GO:00068882 | Colorectum | MSS | endoplasmic reticulum to Golgi vesicle-mediated transport | 44/3467 | 130/18723 | 2.17e-05 | 4.60e-04 | 44 |
GO:00070331 | Colorectum | MSS | vacuole organization | 48/3467 | 180/18723 | 4.32e-03 | 3.07e-02 | 48 |
GO:00481934 | Colorectum | FAP | Golgi vesicle transport | 77/2622 | 296/18723 | 2.86e-08 | 2.62e-06 | 77 |
GO:00162363 | Colorectum | FAP | macroautophagy | 70/2622 | 291/18723 | 2.73e-06 | 1.02e-04 | 70 |
GO:00068884 | Colorectum | FAP | endoplasmic reticulum to Golgi vesicle-mediated transport | 30/2622 | 130/18723 | 3.51e-03 | 2.53e-02 | 30 |
GO:00481935 | Colorectum | CRC | Golgi vesicle transport | 59/2078 | 296/18723 | 5.47e-06 | 2.17e-04 | 59 |
GO:00162364 | Colorectum | CRC | macroautophagy | 51/2078 | 291/18723 | 6.40e-04 | 8.48e-03 | 51 |
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:00162368 | Endometrium | AEH | macroautophagy | 52/2100 | 291/18723 | 4.56e-04 | 4.80e-03 | 52 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
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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. |
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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 |
TRAPPC8 | SNV | Missense_Mutation | c.207G>T | p.Lys69Asn | p.K69N | Q9Y2L5 | protein_coding | deleterious(0) | benign(0.017) | TCGA-L9-A443-01 | Lung | lung adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
TRAPPC8 | SNV | Missense_Mutation | c.2944N>G | p.Lys982Glu | p.K982E | Q9Y2L5 | protein_coding | deleterious(0.05) | benign(0.052) | TCGA-L9-A7SV-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Chemotherapy | cisplatin | CR | |
TRAPPC8 | SNV | Missense_Mutation | c.1382G>C | p.Gly461Ala | p.G461A | Q9Y2L5 | protein_coding | tolerated(0.06) | probably_damaging(0.99) | TCGA-18-3411-01 | Lung | lung squamous cell carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
TRAPPC8 | SNV | Missense_Mutation | novel | c.3130N>A | p.Val1044Ile | p.V1044I | Q9Y2L5 | protein_coding | tolerated(0.12) | benign(0.403) | TCGA-22-1011-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
TRAPPC8 | SNV | Missense_Mutation | rs773906123 | c.617G>A | p.Arg206Lys | p.R206K | Q9Y2L5 | protein_coding | tolerated(0.49) | benign(0.013) | TCGA-39-5016-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
TRAPPC8 | SNV | Missense_Mutation | novel | c.2310G>C | p.Leu770Phe | p.L770F | Q9Y2L5 | protein_coding | tolerated(0.07) | benign(0.019) | TCGA-60-2704-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Chemotherapy | taxotere | PD |
TRAPPC8 | SNV | Missense_Mutation | novel | c.2980N>A | p.Ala994Thr | p.A994T | Q9Y2L5 | protein_coding | tolerated(0.22) | benign(0.06) | TCGA-6A-AB49-01 | Lung | lung squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
TRAPPC8 | SNV | Missense_Mutation | novel | c.2486N>T | p.His829Leu | p.H829L | Q9Y2L5 | protein_coding | tolerated(0.15) | benign(0.003) | TCGA-94-7943-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
TRAPPC8 | SNV | Missense_Mutation | novel | c.719N>C | p.Gln240Pro | p.Q240P | Q9Y2L5 | protein_coding | deleterious(0.03) | benign(0.298) | TCGA-NC-A5HJ-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | cisplatin | PD |
TRAPPC8 | SNV | Missense_Mutation | novel | c.3488N>T | p.Cys1163Phe | p.C1163F | Q9Y2L5 | protein_coding | deleterious(0.03) | benign(0.142) | TCGA-O2-A52Q-01 | Lung | lung squamous cell carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
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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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