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Gene: TRIM54 |
Gene summary for TRIM54 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TRIM54 | Gene ID | 57159 |
| Gene name | tripartite motif containing 54 | |
| Gene Alias | MURF | |
| Cytomap | 2p23.3 | |
| Gene Type | protein-coding | GO ID | GO:0000226 | UniProtAcc | Q9BYV2 |
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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 |
| 57159 | TRIM54 | Pat01-B | Human | Stomach | GC | 6.94e-05 | 1.89e-01 | 0.5754 |
| 57159 | TRIM54 | Pat02-B | Human | Stomach | GC | 1.87e-04 | 1.31e-01 | 0.0368 |
| 57159 | TRIM54 | Pat03-B | Human | Stomach | GC | 7.83e-16 | 3.44e-01 | 0.3693 |
| 57159 | TRIM54 | Pat08-B | Human | Stomach | GC | 1.45e-09 | 4.67e-01 | 0.0182 |
| 57159 | TRIM54 | Pat13-B | Human | Stomach | GC | 8.97e-09 | 2.47e-01 | 0.0555 |
| 57159 | TRIM54 | Pat16-B | Human | Stomach | GC | 7.63e-13 | 3.29e-01 | 0.1918 |
| 57159 | TRIM54 | Pat17-B | Human | Stomach | GC | 2.00e-06 | 2.44e-01 | 0.3109 |
| 57159 | TRIM54 | Pat19-B | Human | Stomach | GC | 9.23e-11 | 2.85e-01 | 0.0826 |
| 57159 | TRIM54 | WIM_2 | Human | Stomach | WIM | 8.96e-09 | 4.82e-01 | 0.1159 |
| 57159 | TRIM54 | SIM_1 | Human | Stomach | SIM | 4.35e-07 | 2.61e-01 | 0.3573 |
| 57159 | TRIM54 | SIM_2 | Human | Stomach | SIM | 2.76e-15 | 4.01e-01 | 0.3139 |
| 57159 | TRIM54 | SIM_3 | Human | Stomach | SIM | 7.12e-04 | 2.37e-01 | 0.0345 |
| 57159 | TRIM54 | SIM_4 | Human | Stomach | SIM | 1.85e-06 | 2.99e-01 | 0.2664 |
| 57159 | TRIM54 | EGC | Human | Stomach | GC | 9.31e-09 | 3.38e-01 | 0.1683 |
| 57159 | TRIM54 | Pt1_Superficial | Human | Stomach | GC | 1.46e-08 | 4.26e-01 | 0.1036 |
| 57159 | TRIM54 | Pt2_Superficial | Human | Stomach | GC | 7.66e-06 | 5.43e-01 | 0.2977 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 |
| ∗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:19029036 | Stomach | GC | regulation of supramolecular fiber organization | 53/1159 | 383/18723 | 3.07e-08 | 2.39e-06 | 53 |
| GO:00106396 | Stomach | GC | negative regulation of organelle organization | 38/1159 | 348/18723 | 4.87e-04 | 7.04e-03 | 38 |
| GO:19029045 | Stomach | GC | negative regulation of supramolecular fiber organization | 21/1159 | 167/18723 | 1.55e-03 | 1.67e-02 | 21 |
| GO:00224116 | Stomach | GC | cellular component disassembly | 42/1159 | 443/18723 | 3.99e-03 | 3.35e-02 | 42 |
| GO:00514945 | Stomach | GC | negative regulation of cytoskeleton organization | 19/1159 | 163/18723 | 5.86e-03 | 4.44e-02 | 19 |
| GO:190290341 | Stomach | WIM | regulation of supramolecular fiber organization | 22/426 | 383/18723 | 7.23e-05 | 2.09e-03 | 22 |
| GO:001063941 | Stomach | WIM | negative regulation of organelle organization | 17/426 | 348/18723 | 2.71e-03 | 3.07e-02 | 17 |
| GO:190290351 | Stomach | SIM | regulation of supramolecular fiber organization | 37/708 | 383/18723 | 1.84e-07 | 1.40e-05 | 37 |
| GO:00106395 | Stomach | SIM | negative regulation of organelle organization | 27/708 | 348/18723 | 3.53e-04 | 6.34e-03 | 27 |
| GO:190290431 | Stomach | SIM | negative regulation of supramolecular fiber organization | 14/708 | 167/18723 | 4.50e-03 | 3.94e-02 | 14 |
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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 |
| TRIM54 | SNV | Missense_Mutation | rs868422808 | c.1087N>A | p.Glu363Lys | p.E363K | Q9BYV2 | protein_coding | tolerated(0.47) | benign(0.001) | TCGA-B6-A402-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | PD |
| TRIM54 | SNV | Missense_Mutation | c.391N>C | p.Glu131Gln | p.E131Q | Q9BYV2 | protein_coding | deleterious(0.04) | benign(0.361) | TCGA-EK-A2PL-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD | |
| TRIM54 | SNV | Missense_Mutation | rs767943141 | c.157G>A | p.Asp53Asn | p.D53N | Q9BYV2 | protein_coding | deleterious(0.02) | benign(0.233) | TCGA-EK-A3GK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| TRIM54 | SNV | Missense_Mutation | rs772619318 | c.1120G>A | p.Ala374Thr | p.A374T | Q9BYV2 | protein_coding | tolerated_low_confidence(0.78) | benign(0.001) | TCGA-VS-A959-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD |
| TRIM54 | SNV | Missense_Mutation | novel | c.99C>A | p.Phe33Leu | p.F33L | Q9BYV2 | protein_coding | deleterious(0) | possibly_damaging(0.872) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TRIM54 | SNV | Missense_Mutation | rs763773532 | c.290G>A | p.Arg97Gln | p.R97Q | Q9BYV2 | protein_coding | deleterious(0.02) | probably_damaging(0.994) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TRIM54 | SNV | Missense_Mutation | c.1089N>T | p.Glu363Asp | p.E363D | Q9BYV2 | protein_coding | tolerated(0.37) | benign(0) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| TRIM54 | SNV | Missense_Mutation | novel | c.914N>G | p.Leu305Arg | p.L305R | Q9BYV2 | protein_coding | deleterious(0.01) | probably_damaging(0.991) | TCGA-CM-5861-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
| TRIM54 | SNV | Missense_Mutation | c.260T>C | p.Leu87Pro | p.L87P | Q9BYV2 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-CM-6163-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| TRIM54 | SNV | Missense_Mutation | rs770394298 | c.506N>A | p.Arg169His | p.R169H | Q9BYV2 | protein_coding | tolerated(0.1) | possibly_damaging(0.615) | TCGA-DM-A1HB-01 | Colorectum | colon adenocarcinoma | Male | >=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 |
| Page: 1 |
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