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Gene: TCOF1 |
Gene summary for TCOF1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TCOF1 | Gene ID | 6949 |
| Gene name | treacle ribosome biogenesis factor 1 | |
| Gene Alias | MFD1 | |
| Cytomap | 5q32-q33.1 | |
| Gene Type | protein-coding | GO ID | GO:0001501 | UniProtAcc | Q13428 |
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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 |
| 6949 | TCOF1 | LZE4T | Human | Esophagus | ESCC | 1.18e-07 | 1.50e-01 | 0.0811 |
| 6949 | TCOF1 | LZE7T | Human | Esophagus | ESCC | 1.26e-05 | 3.23e-01 | 0.0667 |
| 6949 | TCOF1 | LZE8T | Human | Esophagus | ESCC | 9.63e-07 | 9.79e-02 | 0.067 |
| 6949 | TCOF1 | LZE20T | Human | Esophagus | ESCC | 3.65e-03 | 3.91e-02 | 0.0662 |
| 6949 | TCOF1 | LZE24T | Human | Esophagus | ESCC | 1.38e-09 | 3.35e-01 | 0.0596 |
| 6949 | TCOF1 | LZE21T | Human | Esophagus | ESCC | 5.31e-05 | 3.58e-01 | 0.0655 |
| 6949 | TCOF1 | P1T-E | Human | Esophagus | ESCC | 9.59e-03 | 3.23e-01 | 0.0875 |
| 6949 | TCOF1 | P2T-E | Human | Esophagus | ESCC | 2.29e-21 | 6.21e-01 | 0.1177 |
| 6949 | TCOF1 | P4T-E | Human | Esophagus | ESCC | 1.19e-16 | 4.32e-01 | 0.1323 |
| 6949 | TCOF1 | P5T-E | Human | Esophagus | ESCC | 4.06e-25 | 5.37e-01 | 0.1327 |
| 6949 | TCOF1 | P8T-E | Human | Esophagus | ESCC | 4.83e-12 | 1.80e-01 | 0.0889 |
| 6949 | TCOF1 | P9T-E | Human | Esophagus | ESCC | 6.41e-09 | 2.29e-01 | 0.1131 |
| 6949 | TCOF1 | P10T-E | Human | Esophagus | ESCC | 5.16e-16 | 3.16e-01 | 0.116 |
| 6949 | TCOF1 | P11T-E | Human | Esophagus | ESCC | 6.73e-10 | 3.74e-01 | 0.1426 |
| 6949 | TCOF1 | P12T-E | Human | Esophagus | ESCC | 1.83e-17 | 4.46e-01 | 0.1122 |
| 6949 | TCOF1 | P15T-E | Human | Esophagus | ESCC | 6.10e-16 | 4.21e-01 | 0.1149 |
| 6949 | TCOF1 | P16T-E | Human | Esophagus | ESCC | 9.05e-16 | 3.02e-01 | 0.1153 |
| 6949 | TCOF1 | P17T-E | Human | Esophagus | ESCC | 7.62e-11 | 7.21e-01 | 0.1278 |
| 6949 | TCOF1 | P19T-E | Human | Esophagus | ESCC | 1.62e-02 | 4.54e-01 | 0.1662 |
| 6949 | TCOF1 | P20T-E | Human | Esophagus | ESCC | 5.24e-11 | 2.39e-01 | 0.1124 |
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| 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 | ||
| 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:0006417111 | Esophagus | ESCC | regulation of translation | 304/8552 | 468/18723 | 1.53e-17 | 1.33e-15 | 304 |
| GO:00987812 | Esophagus | ESCC | ncRNA transcription | 45/8552 | 56/18723 | 1.05e-07 | 1.72e-06 | 45 |
| GO:00063602 | Esophagus | ESCC | transcription by RNA polymerase I | 42/8552 | 55/18723 | 3.41e-06 | 3.78e-05 | 42 |
| GO:00093032 | Esophagus | ESCC | rRNA transcription | 28/8552 | 34/18723 | 1.21e-05 | 1.12e-04 | 28 |
| GO:00488638 | Esophagus | ESCC | stem cell differentiation | 122/8552 | 206/18723 | 5.95e-05 | 4.59e-04 | 122 |
| GO:00018378 | Esophagus | ESCC | epithelial to mesenchymal transition | 95/8552 | 157/18723 | 1.25e-04 | 8.56e-04 | 95 |
| GO:00487628 | Esophagus | ESCC | mesenchymal cell differentiation | 133/8552 | 236/18723 | 5.94e-04 | 3.22e-03 | 133 |
| GO:00427902 | Esophagus | ESCC | nucleolar large rRNA transcription by RNA polymerase I | 15/8552 | 18/18723 | 1.20e-03 | 5.88e-03 | 15 |
| GO:00604856 | Esophagus | ESCC | mesenchyme development | 156/8552 | 291/18723 | 3.76e-03 | 1.53e-02 | 156 |
| GO:000641712 | Liver | Cirrhotic | regulation of translation | 194/4634 | 468/18723 | 7.28e-16 | 8.79e-14 | 194 |
| GO:004886311 | Liver | Cirrhotic | stem cell differentiation | 66/4634 | 206/18723 | 1.06e-02 | 4.68e-02 | 66 |
| GO:000641722 | Liver | HCC | regulation of translation | 287/7958 | 468/18723 | 8.79e-17 | 8.08e-15 | 287 |
| GO:0009303 | Liver | HCC | rRNA transcription | 25/7958 | 34/18723 | 2.42e-04 | 1.81e-03 | 25 |
| GO:0006360 | Liver | HCC | transcription by RNA polymerase I | 36/7958 | 55/18723 | 4.94e-04 | 3.23e-03 | 36 |
| GO:0098781 | Liver | HCC | ncRNA transcription | 33/7958 | 56/18723 | 9.64e-03 | 3.63e-02 | 33 |
| GO:0042790 | Liver | HCC | nucleolar large rRNA transcription by RNA polymerase I | 13/7958 | 18/18723 | 1.05e-02 | 3.89e-02 | 13 |
| GO:000641720 | Oral cavity | OSCC | regulation of translation | 274/7305 | 468/18723 | 4.39e-18 | 4.63e-16 | 274 |
| GO:00987811 | Oral cavity | OSCC | ncRNA transcription | 38/7305 | 56/18723 | 1.15e-05 | 1.18e-04 | 38 |
| GO:00063601 | Oral cavity | OSCC | transcription by RNA polymerase I | 36/7305 | 55/18723 | 6.42e-05 | 5.22e-04 | 36 |
| GO:00093031 | Oral cavity | OSCC | rRNA transcription | 24/7305 | 34/18723 | 1.89e-04 | 1.28e-03 | 24 |
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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 |
| TCOF1 | SNV | Missense_Mutation | novel | c.3659A>G | p.Lys1220Arg | p.K1220R | Q13428 | protein_coding | deleterious(0.01) | probably_damaging(0.971) | TCGA-A8-A08G-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR |
| TCOF1 | SNV | Missense_Mutation | c.3475N>C | p.Asp1159His | p.D1159H | Q13428 | protein_coding | deleterious(0) | possibly_damaging(0.819) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| TCOF1 | SNV | Missense_Mutation | c.2048N>T | p.Ala683Val | p.A683V | Q13428 | protein_coding | tolerated(0.1) | benign(0.228) | TCGA-BH-A1F6-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| TCOF1 | SNV | Missense_Mutation | c.3707N>T | p.Ala1236Val | p.A1236V | Q13428 | protein_coding | tolerated(0.12) | benign(0.168) | TCGA-E2-A15O-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | PD | |
| TCOF1 | SNV | Missense_Mutation | c.3908N>T | p.Pro1303Leu | p.P1303L | Q13428 | protein_coding | deleterious(0) | possibly_damaging(0.781) | TCGA-E2-A1LG-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| TCOF1 | insertion | Frame_Shift_Ins | novel | c.3661_3662insACCTGACTTTGCTGTTTGA | p.Ala1221AspfsTer26 | p.A1221Dfs*26 | Q13428 | protein_coding | TCGA-A8-A08G-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | ||
| TCOF1 | insertion | Frame_Shift_Ins | novel | c.2394_2395insCT | p.Ala799LeufsTer30 | p.A799Lfs*30 | Q13428 | protein_coding | TCGA-BH-A0DZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | docetaxel | SD | ||
| TCOF1 | deletion | Frame_Shift_Del | novel | c.3639delN | p.Ala1214ProfsTer12 | p.A1214Pfs*12 | Q13428 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| TCOF1 | SNV | Missense_Mutation | c.206C>T | p.Ala69Val | p.A69V | Q13428 | protein_coding | deleterious(0.02) | possibly_damaging(0.801) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| TCOF1 | SNV | Missense_Mutation | novel | c.3695C>T | p.Ser1232Phe | p.S1232F | Q13428 | protein_coding | deleterious(0.02) | possibly_damaging(0.854) | 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 |
| Page: 1 |
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