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Gene: TRIM56 |
Gene summary for TRIM56 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TRIM56 | Gene ID | 81844 |
| Gene name | tripartite motif containing 56 | |
| Gene Alias | RNF109 | |
| Cytomap | 7q22.1 | |
| Gene Type | protein-coding | GO ID | GO:0000209 | UniProtAcc | Q9BRZ2 |
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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 |
| 81844 | TRIM56 | CCI_2 | Human | Cervix | CC | 1.87e-04 | 6.79e-01 | 0.5249 |
| 81844 | TRIM56 | CCI_3 | Human | Cervix | CC | 3.14e-02 | 5.00e-01 | 0.516 |
| 81844 | TRIM56 | HTA11_3410_2000001011 | Human | Colorectum | AD | 4.71e-04 | 2.76e-01 | 0.0155 |
| 81844 | TRIM56 | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.19e-10 | 6.15e-01 | -0.1808 |
| 81844 | TRIM56 | HTA11_1938_2000001011 | Human | Colorectum | AD | 1.06e-10 | 5.70e-01 | -0.0811 |
| 81844 | TRIM56 | HTA11_78_2000001011 | Human | Colorectum | AD | 8.80e-10 | 6.31e-01 | -0.1088 |
| 81844 | TRIM56 | HTA11_347_2000001011 | Human | Colorectum | AD | 4.58e-28 | 8.26e-01 | -0.1954 |
| 81844 | TRIM56 | HTA11_411_2000001011 | Human | Colorectum | SER | 1.10e-06 | 1.14e+00 | -0.2602 |
| 81844 | TRIM56 | HTA11_2112_2000001011 | Human | Colorectum | SER | 4.98e-05 | 8.31e-01 | -0.2196 |
| 81844 | TRIM56 | HTA11_3361_2000001011 | Human | Colorectum | AD | 4.62e-08 | 6.08e-01 | -0.1207 |
| 81844 | TRIM56 | HTA11_83_2000001011 | Human | Colorectum | SER | 1.23e-09 | 6.23e-01 | -0.1526 |
| 81844 | TRIM56 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.47e-30 | 7.85e-01 | -0.1464 |
| 81844 | TRIM56 | HTA11_866_2000001011 | Human | Colorectum | AD | 4.75e-24 | 7.19e-01 | -0.1001 |
| 81844 | TRIM56 | HTA11_1391_2000001011 | Human | Colorectum | AD | 6.33e-19 | 9.06e-01 | -0.059 |
| 81844 | TRIM56 | HTA11_2992_2000001011 | Human | Colorectum | SER | 1.12e-02 | 5.98e-01 | -0.1706 |
| 81844 | TRIM56 | HTA11_546_2000001011 | Human | Colorectum | AD | 5.50e-12 | 8.15e-01 | -0.0842 |
| 81844 | TRIM56 | HTA11_866_3004761011 | Human | Colorectum | AD | 3.61e-19 | 6.67e-01 | 0.096 |
| 81844 | TRIM56 | HTA11_8622_2000001021 | Human | Colorectum | SER | 1.18e-03 | 6.62e-01 | 0.0528 |
| 81844 | TRIM56 | HTA11_7663_2000001011 | Human | Colorectum | SER | 8.83e-04 | 6.87e-01 | 0.0131 |
| 81844 | TRIM56 | HTA11_10623_2000001011 | Human | Colorectum | AD | 9.17e-07 | 7.73e-01 | -0.0177 |
| Page: 1 2 3 4 5 6 7 8 9 |
| 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 | ||
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:00002097 | Cervix | CC | protein polyubiquitination | 58/2311 | 236/18723 | 1.57e-07 | 7.41e-06 | 58 |
| GO:00018197 | Cervix | CC | positive regulation of cytokine production | 95/2311 | 467/18723 | 4.88e-07 | 1.85e-05 | 95 |
| GO:00096158 | Cervix | CC | response to virus | 73/2311 | 367/18723 | 2.22e-05 | 3.95e-04 | 73 |
| GO:00324791 | Cervix | CC | regulation of type I interferon production | 21/2311 | 95/18723 | 5.32e-03 | 3.10e-02 | 21 |
| GO:00326061 | Cervix | CC | type I interferon production | 21/2311 | 95/18723 | 5.32e-03 | 3.10e-02 | 21 |
| GO:00705343 | Cervix | CC | protein K63-linked ubiquitination | 14/2311 | 56/18723 | 6.93e-03 | 3.74e-02 | 14 |
| GO:00324815 | Cervix | CC | positive regulation of type I interferon production | 14/2311 | 58/18723 | 9.57e-03 | 4.73e-02 | 14 |
| GO:00516072 | Cervix | CC | defense response to virus | 46/2311 | 265/18723 | 1.04e-02 | 4.97e-02 | 46 |
| GO:01405462 | Cervix | CC | defense response to symbiont | 46/2311 | 265/18723 | 1.04e-02 | 4.97e-02 | 46 |
| GO:0000209 | Colorectum | AD | protein polyubiquitination | 78/3918 | 236/18723 | 8.71e-06 | 2.06e-04 | 78 |
| GO:0032481 | Colorectum | AD | positive regulation of type I interferon production | 23/3918 | 58/18723 | 8.82e-04 | 8.53e-03 | 23 |
| GO:0034340 | Colorectum | AD | response to type I interferon | 22/3918 | 58/18723 | 2.23e-03 | 1.75e-02 | 22 |
| GO:0070534 | Colorectum | AD | protein K63-linked ubiquitination | 20/3918 | 56/18723 | 7.57e-03 | 4.58e-02 | 20 |
| GO:00002091 | Colorectum | SER | protein polyubiquitination | 58/2897 | 236/18723 | 1.69e-04 | 3.18e-03 | 58 |
| GO:00343401 | Colorectum | SER | response to type I interferon | 17/2897 | 58/18723 | 5.50e-03 | 4.07e-02 | 17 |
| GO:00002092 | Colorectum | MSS | protein polyubiquitination | 72/3467 | 236/18723 | 5.19e-06 | 1.42e-04 | 72 |
| GO:00705341 | Colorectum | MSS | protein K63-linked ubiquitination | 21/3467 | 56/18723 | 6.51e-04 | 7.06e-03 | 21 |
| GO:00324811 | Colorectum | MSS | positive regulation of type I interferon production | 20/3467 | 58/18723 | 2.82e-03 | 2.20e-02 | 20 |
| GO:00343402 | Colorectum | MSS | response to type I interferon | 20/3467 | 58/18723 | 2.82e-03 | 2.20e-02 | 20 |
| GO:00343403 | Colorectum | MSI-H | response to type I interferon | 13/1319 | 58/18723 | 1.58e-04 | 4.52e-03 | 13 |
| Page: 1 2 3 4 5 |
| 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 |
| 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 |
| TRIM56 | SNV | Missense_Mutation | c.1525C>G | p.Arg509Gly | p.R509G | Q9BRZ2 | protein_coding | deleterious(0.01) | benign(0.238) | TCGA-A8-A06X-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TRIM56 | SNV | Missense_Mutation | c.49N>T | p.Asp17Tyr | p.D17Y | Q9BRZ2 | protein_coding | deleterious(0) | probably_damaging(0.968) | TCGA-AO-A124-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| TRIM56 | SNV | Missense_Mutation | c.1534N>A | p.Gly512Arg | p.G512R | Q9BRZ2 | protein_coding | deleterious(0) | probably_damaging(0.981) | TCGA-D8-A1Y1-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | tamoxiphen | PD | |
| TRIM56 | SNV | Missense_Mutation | novel | c.1594N>G | p.Lys532Glu | p.K532E | Q9BRZ2 | protein_coding | deleterious(0) | possibly_damaging(0.803) | TCGA-E2-A155-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD |
| TRIM56 | insertion | Nonsense_Mutation | novel | c.59_60insTCAAACTCTCGGTTTGATGATGTGGCATTTAGCATGAGTGA | p.Cys21GlnfsTer12 | p.C21Qfs*12 | Q9BRZ2 | protein_coding | TCGA-A8-A07J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | ||
| TRIM56 | SNV | Missense_Mutation | rs200430251 | c.1831G>A | p.Val611Met | p.V611M | Q9BRZ2 | protein_coding | deleterious(0) | probably_damaging(0.988) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| TRIM56 | SNV | Missense_Mutation | c.397N>T | p.Asp133Tyr | p.D133Y | Q9BRZ2 | protein_coding | deleterious(0.03) | probably_damaging(0.984) | TCGA-C5-A1BL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| TRIM56 | SNV | Missense_Mutation | novel | c.1462N>A | p.Leu488Ile | p.L488I | Q9BRZ2 | protein_coding | tolerated(0.07) | possibly_damaging(0.522) | TCGA-VS-A9UJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD |
| TRIM56 | SNV | Missense_Mutation | c.1864N>T | p.Thr622Ser | p.T622S | Q9BRZ2 | protein_coding | tolerated(0.95) | probably_damaging(0.935) | TCGA-A6-5666-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| TRIM56 | SNV | Missense_Mutation | rs546901188 | c.2252G>A | p.Arg751His | p.R751H | Q9BRZ2 | protein_coding | deleterious_low_confidence(0.03) | benign(0.382) | TCGA-AA-3492-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 |
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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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