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Gene: TRAPPC6B |
Gene summary for TRAPPC6B |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TRAPPC6B | Gene ID | 122553 |
| Gene name | trafficking protein particle complex subunit 6B | |
| Gene Alias | NEDMEBA | |
| Cytomap | 14q21.1 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | Q86SZ2 |
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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 |
| 122553 | TRAPPC6B | LZE4T | Human | Esophagus | ESCC | 1.57e-19 | 5.62e-01 | 0.0811 |
| 122553 | TRAPPC6B | LZE5T | Human | Esophagus | ESCC | 7.45e-04 | 5.99e-01 | 0.0514 |
| 122553 | TRAPPC6B | LZE7T | Human | Esophagus | ESCC | 5.67e-04 | 2.98e-01 | 0.0667 |
| 122553 | TRAPPC6B | LZE8T | Human | Esophagus | ESCC | 6.20e-05 | 1.37e-01 | 0.067 |
| 122553 | TRAPPC6B | LZE20T | Human | Esophagus | ESCC | 5.67e-04 | 1.87e-01 | 0.0662 |
| 122553 | TRAPPC6B | LZE22T | Human | Esophagus | ESCC | 2.61e-03 | 4.13e-01 | 0.068 |
| 122553 | TRAPPC6B | LZE24T | Human | Esophagus | ESCC | 4.69e-12 | 3.56e-01 | 0.0596 |
| 122553 | TRAPPC6B | LZE21T | Human | Esophagus | ESCC | 3.36e-04 | 3.55e-01 | 0.0655 |
| 122553 | TRAPPC6B | LZE6T | Human | Esophagus | ESCC | 9.73e-04 | 2.58e-01 | 0.0845 |
| 122553 | TRAPPC6B | P1T-E | Human | Esophagus | ESCC | 4.04e-09 | 5.32e-01 | 0.0875 |
| 122553 | TRAPPC6B | P2T-E | Human | Esophagus | ESCC | 1.18e-23 | 4.12e-01 | 0.1177 |
| 122553 | TRAPPC6B | P4T-E | Human | Esophagus | ESCC | 4.31e-22 | 5.02e-01 | 0.1323 |
| 122553 | TRAPPC6B | P5T-E | Human | Esophagus | ESCC | 1.62e-22 | 3.91e-01 | 0.1327 |
| 122553 | TRAPPC6B | P8T-E | Human | Esophagus | ESCC | 6.91e-69 | 1.02e+00 | 0.0889 |
| 122553 | TRAPPC6B | P9T-E | Human | Esophagus | ESCC | 8.58e-10 | 2.31e-01 | 0.1131 |
| 122553 | TRAPPC6B | P10T-E | Human | Esophagus | ESCC | 2.17e-38 | 5.72e-01 | 0.116 |
| 122553 | TRAPPC6B | P11T-E | Human | Esophagus | ESCC | 1.96e-16 | 5.88e-01 | 0.1426 |
| 122553 | TRAPPC6B | P12T-E | Human | Esophagus | ESCC | 1.51e-125 | 2.42e+00 | 0.1122 |
| 122553 | TRAPPC6B | P15T-E | Human | Esophagus | ESCC | 2.35e-42 | 9.57e-01 | 0.1149 |
| 122553 | TRAPPC6B | P16T-E | Human | Esophagus | ESCC | 2.62e-30 | 4.89e-01 | 0.1153 |
| Page: 1 2 3 4 |
| 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma |
| ∗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: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:004308715 | Esophagus | ESCC | regulation of GTPase activity | 183/8552 | 348/18723 | 5.34e-03 | 2.00e-02 | 183 |
| 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:004308710 | Oral cavity | OSCC | regulation of GTPase activity | 165/7305 | 348/18723 | 7.94e-04 | 4.27e-03 | 165 |
| 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 |
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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 |
| TRAPPC6B | SNV | Missense_Mutation | rs763287802 | c.77N>G | p.Glu26Gly | p.E26G | Q86SZ2 | protein_coding | tolerated(0.17) | benign(0.19) | TCGA-ZJ-AAX8-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD |
| TRAPPC6B | SNV | Missense_Mutation | novel | c.410N>T | p.Ser137Ile | p.S137I | Q86SZ2 | protein_coding | deleterious(0) | probably_damaging(0.937) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TRAPPC6B | SNV | Missense_Mutation | novel | c.92N>A | p.Arg31Gln | p.R31Q | Q86SZ2 | protein_coding | tolerated(0.47) | benign(0.063) | TCGA-AJ-A3EL-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TRAPPC6B | SNV | Missense_Mutation | c.187G>T | p.Asp63Tyr | p.D63Y | Q86SZ2 | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-AP-A056-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| TRAPPC6B | SNV | Missense_Mutation | novel | c.365N>T | p.Thr122Met | p.T122M | Q86SZ2 | protein_coding | deleterious(0.04) | possibly_damaging(0.84) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TRAPPC6B | SNV | Missense_Mutation | novel | c.19N>C | p.Phe7Leu | p.F7L | Q86SZ2 | protein_coding | tolerated(0.14) | probably_damaging(0.999) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TRAPPC6B | SNV | Missense_Mutation | c.211G>T | p.Asp71Tyr | p.D71Y | Q86SZ2 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-B5-A0JY-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD | |
| TRAPPC6B | SNV | Missense_Mutation | novel | c.365C>T | p.Thr122Met | p.T122M | Q86SZ2 | protein_coding | deleterious(0.04) | possibly_damaging(0.84) | TCGA-B5-A3FC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TRAPPC6B | SNV | Missense_Mutation | novel | c.92N>A | p.Arg31Gln | p.R31Q | Q86SZ2 | protein_coding | tolerated(0.47) | benign(0.063) | TCGA-EO-A22R-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TRAPPC6B | SNV | Missense_Mutation | rs757748410 | c.160N>T | p.Asp54Tyr | p.D54Y | Q86SZ2 | protein_coding | deleterious(0) | probably_damaging(0.99) | TCGA-EO-A22X-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unspecific | Carboplatin | Complete Response |
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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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