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Gene: TRAFD1 |
Gene summary for TRAFD1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TRAFD1 | Gene ID | 10906 |
| Gene name | TRAF-type zinc finger domain containing 1 | |
| Gene Alias | FLN29 | |
| Cytomap | 12q24.13 | |
| Gene Type | protein-coding | GO ID | GO:0002376 | UniProtAcc | A0A024RBK4 |
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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 |
| 10906 | TRAFD1 | LZE4T | Human | Esophagus | ESCC | 2.26e-06 | 1.97e-01 | 0.0811 |
| 10906 | TRAFD1 | LZE7T | Human | Esophagus | ESCC | 2.09e-02 | 1.75e-01 | 0.0667 |
| 10906 | TRAFD1 | LZE8T | Human | Esophagus | ESCC | 2.11e-03 | 1.59e-01 | 0.067 |
| 10906 | TRAFD1 | LZE20T | Human | Esophagus | ESCC | 6.01e-10 | 1.97e-01 | 0.0662 |
| 10906 | TRAFD1 | LZE24T | Human | Esophagus | ESCC | 2.85e-18 | 5.29e-01 | 0.0596 |
| 10906 | TRAFD1 | P1T-E | Human | Esophagus | ESCC | 5.83e-04 | 3.57e-01 | 0.0875 |
| 10906 | TRAFD1 | P2T-E | Human | Esophagus | ESCC | 8.75e-40 | 8.01e-01 | 0.1177 |
| 10906 | TRAFD1 | P4T-E | Human | Esophagus | ESCC | 9.29e-12 | 3.24e-01 | 0.1323 |
| 10906 | TRAFD1 | P5T-E | Human | Esophagus | ESCC | 1.03e-07 | 8.19e-02 | 0.1327 |
| 10906 | TRAFD1 | P8T-E | Human | Esophagus | ESCC | 4.72e-26 | 6.27e-01 | 0.0889 |
| 10906 | TRAFD1 | P9T-E | Human | Esophagus | ESCC | 7.22e-06 | 9.50e-02 | 0.1131 |
| 10906 | TRAFD1 | P10T-E | Human | Esophagus | ESCC | 1.39e-21 | 1.77e-01 | 0.116 |
| 10906 | TRAFD1 | P11T-E | Human | Esophagus | ESCC | 4.46e-17 | 4.99e-01 | 0.1426 |
| 10906 | TRAFD1 | P12T-E | Human | Esophagus | ESCC | 1.07e-18 | 2.36e-01 | 0.1122 |
| 10906 | TRAFD1 | P15T-E | Human | Esophagus | ESCC | 4.82e-12 | 3.02e-01 | 0.1149 |
| 10906 | TRAFD1 | P16T-E | Human | Esophagus | ESCC | 1.04e-20 | 4.32e-01 | 0.1153 |
| 10906 | TRAFD1 | P17T-E | Human | Esophagus | ESCC | 5.03e-04 | 3.13e-01 | 0.1278 |
| 10906 | TRAFD1 | P19T-E | Human | Esophagus | ESCC | 8.69e-03 | 4.71e-01 | 0.1662 |
| 10906 | TRAFD1 | P20T-E | Human | Esophagus | ESCC | 5.22e-21 | 4.63e-01 | 0.1124 |
| 10906 | TRAFD1 | P21T-E | Human | Esophagus | ESCC | 1.57e-21 | 2.73e-01 | 0.1617 |
| Page: 1 2 3 4 5 |
| 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 |
| ∗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:00028318 | Esophagus | ESCC | regulation of response to biotic stimulus | 191/8552 | 327/18723 | 2.12e-06 | 2.45e-05 | 191 |
| GO:000283212 | Esophagus | ESCC | negative regulation of response to biotic stimulus | 72/8552 | 108/18723 | 8.36e-06 | 8.11e-05 | 72 |
| GO:00450885 | Esophagus | ESCC | regulation of innate immune response | 125/8552 | 218/18723 | 3.34e-04 | 1.96e-03 | 125 |
| GO:00507775 | Esophagus | ESCC | negative regulation of immune response | 112/8552 | 194/18723 | 4.67e-04 | 2.62e-03 | 112 |
| GO:000268316 | Esophagus | ESCC | negative regulation of immune system process | 231/8552 | 434/18723 | 8.48e-04 | 4.36e-03 | 231 |
| GO:00458245 | Esophagus | ESCC | negative regulation of innate immune response | 45/8552 | 71/18723 | 1.98e-03 | 8.90e-03 | 45 |
| GO:00028321 | Liver | HCC | negative regulation of response to biotic stimulus | 66/7958 | 108/18723 | 7.24e-05 | 6.50e-04 | 66 |
| GO:00028312 | Liver | HCC | regulation of response to biotic stimulus | 173/7958 | 327/18723 | 8.55e-05 | 7.48e-04 | 173 |
| GO:00450881 | Liver | HCC | regulation of innate immune response | 113/7958 | 218/18723 | 3.27e-03 | 1.50e-02 | 113 |
| GO:00458241 | Liver | HCC | negative regulation of innate immune response | 42/7958 | 71/18723 | 3.41e-03 | 1.55e-02 | 42 |
| GO:0050777 | Liver | HCC | negative regulation of immune response | 101/7958 | 194/18723 | 4.40e-03 | 1.90e-02 | 101 |
| GO:00028317 | Oral cavity | OSCC | regulation of response to biotic stimulus | 177/7305 | 327/18723 | 1.73e-08 | 3.43e-07 | 177 |
| GO:00028324 | Oral cavity | OSCC | negative regulation of response to biotic stimulus | 65/7305 | 108/18723 | 6.62e-06 | 7.29e-05 | 65 |
| GO:00450884 | Oral cavity | OSCC | regulation of innate immune response | 116/7305 | 218/18723 | 1.36e-05 | 1.37e-04 | 116 |
| GO:000268310 | Oral cavity | OSCC | negative regulation of immune system process | 204/7305 | 434/18723 | 3.72e-04 | 2.27e-03 | 204 |
| GO:00458244 | Oral cavity | OSCC | negative regulation of innate immune response | 41/7305 | 71/18723 | 1.05e-03 | 5.40e-03 | 41 |
| GO:00507774 | Oral cavity | OSCC | negative regulation of immune response | 97/7305 | 194/18723 | 1.16e-03 | 5.91e-03 | 97 |
| GO:000283211 | Oral cavity | LP | negative regulation of response to biotic stimulus | 46/4623 | 108/18723 | 3.31e-05 | 5.02e-04 | 46 |
| GO:004508811 | Oral cavity | LP | regulation of innate immune response | 78/4623 | 218/18723 | 1.57e-04 | 1.78e-03 | 78 |
| GO:000283112 | Oral cavity | LP | regulation of response to biotic stimulus | 109/4623 | 327/18723 | 2.45e-04 | 2.60e-03 | 109 |
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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 |
| TRAFD1 | SNV | Missense_Mutation | novel | c.949G>C | p.Ala317Pro | p.A317P | O14545 | protein_coding | deleterious(0) | probably_damaging(0.993) | TCGA-A7-A6VW-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | CR |
| TRAFD1 | SNV | Missense_Mutation | c.368N>G | p.Val123Gly | p.V123G | O14545 | protein_coding | deleterious(0) | benign(0.283) | TCGA-A8-A07I-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | 5-fluorouracil | CR | |
| TRAFD1 | SNV | Missense_Mutation | c.838N>T | p.Ser280Cys | p.S280C | O14545 | protein_coding | deleterious(0.01) | benign(0.035) | TCGA-BH-A0B4-01 | Breast | breast invasive carcinoma | Male | >=65 | III/IV | Hormone Therapy | tamoxiphen | SD | |
| TRAFD1 | SNV | Missense_Mutation | novel | c.181N>G | p.Gln61Glu | p.Q61E | O14545 | protein_coding | deleterious(0.03) | possibly_damaging(0.7) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TRAFD1 | SNV | Missense_Mutation | c.889G>A | p.Glu297Lys | p.E297K | O14545 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-BH-A209-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TRAFD1 | SNV | Missense_Mutation | c.1371N>A | p.Asn457Lys | p.N457K | O14545 | protein_coding | deleterious(0.01) | possibly_damaging(0.813) | TCGA-D8-A1JK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TRAFD1 | SNV | Missense_Mutation | c.1159N>T | p.Asp387Tyr | p.D387Y | O14545 | protein_coding | deleterious(0.01) | probably_damaging(0.999) | TCGA-E2-A1LH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| TRAFD1 | insertion | In_Frame_Ins | novel | c.1230_1231insATTGGAAAT | p.Gln410_Pro411insIleGlyAsn | p.Q410_P411insIGN | O14545 | protein_coding | TCGA-BH-A0AY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | SD | |||
| TRAFD1 | insertion | Nonsense_Mutation | novel | c.1231_1232insATCATTCTCAGTAAA | p.Pro411delinsHisHisSerGlnTerThr | p.P411delinsHHSQ*T | O14545 | protein_coding | TCGA-BH-A0AY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | SD | |||
| TRAFD1 | SNV | Missense_Mutation | rs755087454 | c.1676N>A | p.Arg559His | p.R559H | O14545 | protein_coding | tolerated(0.13) | benign(0.023) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
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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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