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Gene: TMF1 |
Gene summary for TMF1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TMF1 | Gene ID | 7110 |
| Gene name | TATA element modulatory factor 1 | |
| Gene Alias | ARA160 | |
| Cytomap | 3p14.1 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | A0A024R370 |
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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 |
| 7110 | TMF1 | LZE4T | Human | Esophagus | ESCC | 1.68e-17 | 4.69e-01 | 0.0811 |
| 7110 | TMF1 | LZE5T | Human | Esophagus | ESCC | 6.23e-05 | 4.06e-01 | 0.0514 |
| 7110 | TMF1 | LZE7T | Human | Esophagus | ESCC | 4.58e-04 | 1.58e-01 | 0.0667 |
| 7110 | TMF1 | LZE24T | Human | Esophagus | ESCC | 1.11e-23 | 6.70e-01 | 0.0596 |
| 7110 | TMF1 | LZE21T | Human | Esophagus | ESCC | 1.05e-05 | 2.99e-01 | 0.0655 |
| 7110 | TMF1 | LZE6T | Human | Esophagus | ESCC | 9.62e-08 | 2.02e-01 | 0.0845 |
| 7110 | TMF1 | P1T-E | Human | Esophagus | ESCC | 1.15e-05 | 3.86e-01 | 0.0875 |
| 7110 | TMF1 | P2T-E | Human | Esophagus | ESCC | 1.53e-37 | 7.55e-01 | 0.1177 |
| 7110 | TMF1 | P4T-E | Human | Esophagus | ESCC | 6.67e-28 | 7.12e-01 | 0.1323 |
| 7110 | TMF1 | P5T-E | Human | Esophagus | ESCC | 1.35e-10 | 2.34e-01 | 0.1327 |
| 7110 | TMF1 | P8T-E | Human | Esophagus | ESCC | 7.14e-19 | 3.63e-01 | 0.0889 |
| 7110 | TMF1 | P9T-E | Human | Esophagus | ESCC | 6.56e-13 | 3.43e-01 | 0.1131 |
| 7110 | TMF1 | P10T-E | Human | Esophagus | ESCC | 3.33e-19 | 4.20e-01 | 0.116 |
| 7110 | TMF1 | P11T-E | Human | Esophagus | ESCC | 3.42e-13 | 5.21e-01 | 0.1426 |
| 7110 | TMF1 | P12T-E | Human | Esophagus | ESCC | 6.70e-16 | 4.41e-01 | 0.1122 |
| 7110 | TMF1 | P15T-E | Human | Esophagus | ESCC | 8.86e-15 | 2.87e-01 | 0.1149 |
| 7110 | TMF1 | P16T-E | Human | Esophagus | ESCC | 2.80e-20 | 4.70e-01 | 0.1153 |
| 7110 | TMF1 | P17T-E | Human | Esophagus | ESCC | 3.44e-05 | 3.61e-01 | 0.1278 |
| 7110 | TMF1 | P19T-E | Human | Esophagus | ESCC | 9.11e-05 | 6.59e-01 | 0.1662 |
| 7110 | TMF1 | P20T-E | Human | Esophagus | ESCC | 2.77e-07 | 2.38e-01 | 0.1124 |
| Page: 1 2 3 4 5 6 7 |
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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:000181917 | Skin | AK | positive regulation of cytokine production | 67/1910 | 467/18723 | 2.59e-03 | 1.67e-02 | 67 |
| GO:001605010 | Skin | AK | vesicle organization | 45/1910 | 300/18723 | 5.44e-03 | 3.02e-02 | 45 |
| GO:00109273 | Skin | AK | cellular component assembly involved in morphogenesis | 20/1910 | 107/18723 | 5.45e-03 | 3.02e-02 | 20 |
| GO:001049828 | Skin | cSCC | proteasomal protein catabolic process | 243/4864 | 490/18723 | 7.85e-30 | 4.10e-27 | 243 |
| GO:004217629 | Skin | cSCC | regulation of protein catabolic process | 198/4864 | 391/18723 | 6.03e-26 | 1.89e-23 | 198 |
| GO:190336229 | Skin | cSCC | regulation of cellular protein catabolic process | 139/4864 | 255/18723 | 2.06e-22 | 4.17e-20 | 139 |
| GO:190305029 | Skin | cSCC | regulation of proteolysis involved in cellular protein catabolic process | 121/4864 | 221/18723 | 6.75e-20 | 1.01e-17 | 121 |
| GO:006113629 | Skin | cSCC | regulation of proteasomal protein catabolic process | 106/4864 | 187/18723 | 4.31e-19 | 5.87e-17 | 106 |
| GO:001605015 | Skin | cSCC | vesicle organization | 135/4864 | 300/18723 | 5.98e-13 | 3.44e-11 | 135 |
| GO:004854529 | Skin | cSCC | response to steroid hormone | 135/4864 | 339/18723 | 1.34e-08 | 4.09e-07 | 135 |
| GO:003052227 | Skin | cSCC | intracellular receptor signaling pathway | 108/4864 | 265/18723 | 9.21e-08 | 2.21e-06 | 108 |
| GO:0030518110 | Skin | cSCC | intracellular steroid hormone receptor signaling pathway | 56/4864 | 116/18723 | 1.97e-07 | 4.28e-06 | 56 |
| GO:00069976 | Skin | cSCC | nucleus organization | 62/4864 | 133/18723 | 2.21e-07 | 4.72e-06 | 62 |
| GO:0071383111 | Skin | cSCC | cellular response to steroid hormone stimulus | 84/4864 | 204/18723 | 1.44e-06 | 2.48e-05 | 84 |
| GO:0043401110 | Skin | cSCC | steroid hormone mediated signaling pathway | 60/4864 | 136/18723 | 3.33e-06 | 5.10e-05 | 60 |
| GO:006145825 | Skin | cSCC | reproductive system development | 149/4864 | 427/18723 | 2.30e-05 | 2.65e-04 | 149 |
| GO:004860824 | Skin | cSCC | reproductive structure development | 148/4864 | 424/18723 | 2.40e-05 | 2.74e-04 | 148 |
| GO:0030521110 | Skin | cSCC | androgen receptor signaling pathway | 24/4864 | 44/18723 | 5.16e-05 | 5.28e-04 | 24 |
| GO:000975518 | Skin | cSCC | hormone-mediated signaling pathway | 72/4864 | 190/18723 | 1.92e-04 | 1.61e-03 | 72 |
| GO:00085845 | Skin | cSCC | male gonad development | 51/4864 | 141/18723 | 4.70e-03 | 2.40e-02 | 51 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| 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 |
| TMF1 | SNV | Missense_Mutation | novel | c.467N>A | p.Ser156Tyr | p.S156Y | P82094 | protein_coding | deleterious_low_confidence(0.01) | benign(0.044) | TCGA-A2-A25A-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Cytoxan | SD |
| TMF1 | SNV | Missense_Mutation | novel | c.1513N>G | p.Gln505Glu | p.Q505E | P82094 | protein_coding | deleterious(0.02) | benign(0.214) | TCGA-A7-A4SA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | CR |
| TMF1 | SNV | Missense_Mutation | rs764372262 | c.356N>T | p.Pro119Leu | p.P119L | P82094 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.895) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| TMF1 | SNV | Missense_Mutation | rs760281565 | c.1961N>A | p.Arg654Gln | p.R654Q | P82094 | protein_coding | deleterious(0.02) | probably_damaging(0.973) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TMF1 | SNV | Missense_Mutation | c.1117N>A | p.Ala373Thr | p.A373T | P82094 | protein_coding | tolerated_low_confidence(0.54) | benign(0) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | |
| TMF1 | SNV | Missense_Mutation | c.437N>G | p.Glu146Gly | p.E146G | P82094 | protein_coding | tolerated_low_confidence(0.05) | benign(0.05) | TCGA-E2-A1B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Adriamycin | SD | |
| TMF1 | insertion | Nonsense_Mutation | novel | c.228_229insGGAGTGTAAGTGAAATCAATTCAGATGAT | p.Ser77GlyfsTer3 | p.S77Gfs*3 | P82094 | protein_coding | TCGA-A2-A0EO-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| TMF1 | insertion | Frame_Shift_Ins | novel | c.638_639insAACAGCTCCCTCTTTTGACTGTGCTAGGATGCACCACG | p.Ser214ThrfsTer25 | p.S214Tfs*25 | P82094 | protein_coding | TCGA-A7-A0CJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| TMF1 | deletion | Frame_Shift_Del | novel | c.2611delN | p.Glu871LysfsTer3 | p.E871Kfs*3 | P82094 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| TMF1 | SNV | Missense_Mutation | c.2382G>T | p.Lys794Asn | p.K794N | P82094 | protein_coding | deleterious(0) | probably_damaging(0.972) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
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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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