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Gene: TCAF1 |
Gene summary for TCAF1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TCAF1 | Gene ID | 9747 |
| Gene name | TRPM8 channel associated factor 1 | |
| Gene Alias | FAM115A | |
| Cytomap | 7q35 | |
| Gene Type | protein-coding | GO ID | GO:0006605 | UniProtAcc | Q9Y4C2 |
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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 |
| 9747 | TCAF1 | HTA11_1938_2000001011 | Human | Colorectum | AD | 4.04e-03 | 2.85e-01 | -0.0811 |
| 9747 | TCAF1 | HTA11_78_2000001011 | Human | Colorectum | AD | 1.99e-11 | 4.91e-01 | -0.1088 |
| 9747 | TCAF1 | HTA11_347_2000001011 | Human | Colorectum | AD | 7.36e-20 | 5.34e-01 | -0.1954 |
| 9747 | TCAF1 | HTA11_1391_2000001011 | Human | Colorectum | AD | 2.83e-10 | 4.55e-01 | -0.059 |
| 9747 | TCAF1 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 2.93e-06 | 4.50e-01 | 0.281 |
| 9747 | TCAF1 | A015-C-203 | Human | Colorectum | FAP | 7.28e-05 | -1.10e-01 | -0.1294 |
| 9747 | TCAF1 | A015-C-104 | Human | Colorectum | FAP | 1.00e-04 | -6.44e-02 | -0.1899 |
| 9747 | TCAF1 | A002-C-116 | Human | Colorectum | FAP | 4.39e-06 | -4.74e-02 | -0.0452 |
| 9747 | TCAF1 | F072B | Human | Colorectum | FAP | 3.34e-02 | 3.97e-01 | 0.257 |
| 9747 | TCAF1 | CRC-3-11773 | Human | Colorectum | CRC | 8.23e-03 | -1.19e-01 | 0.2564 |
| 9747 | TCAF1 | LZE2T | Human | Esophagus | ESCC | 1.80e-02 | 5.54e-01 | 0.082 |
| 9747 | TCAF1 | LZE4T | Human | Esophagus | ESCC | 1.58e-04 | 2.07e-01 | 0.0811 |
| 9747 | TCAF1 | LZE7T | Human | Esophagus | ESCC | 3.18e-07 | 3.61e-01 | 0.0667 |
| 9747 | TCAF1 | LZE8T | Human | Esophagus | ESCC | 9.22e-05 | 1.90e-01 | 0.067 |
| 9747 | TCAF1 | LZE20T | Human | Esophagus | ESCC | 8.90e-06 | 1.43e-01 | 0.0662 |
| 9747 | TCAF1 | LZE22T | Human | Esophagus | ESCC | 6.92e-04 | 2.54e-01 | 0.068 |
| 9747 | TCAF1 | LZE24T | Human | Esophagus | ESCC | 5.37e-12 | 3.13e-01 | 0.0596 |
| 9747 | TCAF1 | P1T-E | Human | Esophagus | ESCC | 2.61e-08 | 2.94e-01 | 0.0875 |
| 9747 | TCAF1 | P2T-E | Human | Esophagus | ESCC | 8.33e-15 | 2.60e-01 | 0.1177 |
| 9747 | TCAF1 | P4T-E | Human | Esophagus | ESCC | 2.52e-17 | 3.55e-01 | 0.1323 |
| Page: 1 2 3 4 5 6 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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:003238615 | Oral cavity | OSCC | regulation of intracellular transport | 218/7305 | 337/18723 | 6.91e-22 | 1.41e-19 | 218 |
| GO:000660520 | Oral cavity | OSCC | protein targeting | 204/7305 | 314/18723 | 6.78e-21 | 1.13e-18 | 204 |
| GO:003315718 | Oral cavity | OSCC | regulation of intracellular protein transport | 155/7305 | 229/18723 | 1.05e-18 | 1.28e-16 | 155 |
| GO:190382920 | Oral cavity | OSCC | positive regulation of cellular protein localization | 179/7305 | 276/18723 | 2.20e-18 | 2.41e-16 | 179 |
| GO:190495119 | Oral cavity | OSCC | positive regulation of establishment of protein localization | 196/7305 | 319/18723 | 2.89e-16 | 2.20e-14 | 196 |
| GO:005122219 | Oral cavity | OSCC | positive regulation of protein transport | 187/7305 | 303/18723 | 7.37e-16 | 5.49e-14 | 187 |
| GO:003238818 | Oral cavity | OSCC | positive regulation of intracellular transport | 134/7305 | 202/18723 | 2.82e-15 | 1.88e-13 | 134 |
| GO:009015018 | Oral cavity | OSCC | establishment of protein localization to membrane | 163/7305 | 260/18723 | 7.13e-15 | 4.47e-13 | 163 |
| GO:009031610 | Oral cavity | OSCC | positive regulation of intracellular protein transport | 110/7305 | 160/18723 | 2.10e-14 | 1.19e-12 | 110 |
| GO:190547516 | Oral cavity | OSCC | regulation of protein localization to membrane | 105/7305 | 175/18723 | 1.42e-08 | 2.85e-07 | 105 |
| GO:190547716 | Oral cavity | OSCC | positive regulation of protein localization to membrane | 65/7305 | 106/18723 | 2.69e-06 | 3.32e-05 | 65 |
| GO:19035337 | Oral cavity | OSCC | regulation of protein targeting | 51/7305 | 81/18723 | 1.08e-05 | 1.13e-04 | 51 |
| GO:00066123 | Oral cavity | OSCC | protein targeting to membrane | 75/7305 | 131/18723 | 1.72e-05 | 1.69e-04 | 75 |
| GO:0006605110 | Oral cavity | LP | protein targeting | 156/4623 | 314/18723 | 5.43e-22 | 1.62e-19 | 156 |
| GO:009015019 | Oral cavity | LP | establishment of protein localization to membrane | 128/4623 | 260/18723 | 7.19e-18 | 1.19e-15 | 128 |
| GO:1903829110 | Oral cavity | LP | positive regulation of cellular protein localization | 127/4623 | 276/18723 | 7.52e-15 | 9.81e-13 | 127 |
| GO:003238616 | Oral cavity | LP | regulation of intracellular transport | 145/4623 | 337/18723 | 8.58e-14 | 8.27e-12 | 145 |
| GO:003238819 | Oral cavity | LP | positive regulation of intracellular transport | 97/4623 | 202/18723 | 4.79e-13 | 4.30e-11 | 97 |
| GO:003315719 | Oral cavity | LP | regulation of intracellular protein transport | 106/4623 | 229/18723 | 7.85e-13 | 6.68e-11 | 106 |
| GO:1904951110 | Oral cavity | LP | positive regulation of establishment of protein localization | 132/4623 | 319/18723 | 3.06e-11 | 2.00e-09 | 132 |
| Page: 1 2 3 4 5 6 7 8 9 10 |
| 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 |
| TCAF1 | SNV | Missense_Mutation | novel | c.82N>A | p.Glu28Lys | p.E28K | Q9Y4C2 | protein_coding | tolerated(0.14) | benign(0.348) | TCGA-E2-A2P6-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD |
| TCAF1 | SNV | Missense_Mutation | novel | c.2299G>A | p.Glu767Lys | p.E767K | Q9Y4C2 | protein_coding | tolerated(0.17) | benign(0.028) | TCGA-EA-A3HS-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| TCAF1 | SNV | Missense_Mutation | c.276N>G | p.Ile92Met | p.I92M | Q9Y4C2 | protein_coding | deleterious(0.02) | benign(0.271) | TCGA-CA-6718-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD | |
| TCAF1 | SNV | Missense_Mutation | rs149141329 | c.167N>A | p.Arg56His | p.R56H | Q9Y4C2 | protein_coding | tolerated(0.07) | benign(0.006) | TCGA-CM-4746-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| TCAF1 | SNV | Missense_Mutation | novel | c.316G>A | p.Glu106Lys | p.E106K | Q9Y4C2 | protein_coding | tolerated(0.93) | benign(0.005) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| TCAF1 | SNV | Missense_Mutation | rs373629994 | c.25G>A | p.Glu9Lys | p.E9K | Q9Y4C2 | protein_coding | tolerated(0.1) | benign(0.117) | TCGA-A5-A2K5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TCAF1 | SNV | Missense_Mutation | novel | c.295N>A | p.Ala99Thr | p.A99T | Q9Y4C2 | protein_coding | tolerated(0.55) | benign(0.003) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
| TCAF1 | SNV | Missense_Mutation | novel | c.2613N>T | p.Lys871Asn | p.K871N | Q9Y4C2 | protein_coding | deleterious(0.01) | possibly_damaging(0.701) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TCAF1 | SNV | Missense_Mutation | novel | c.2312C>T | p.Pro771Leu | p.P771L | Q9Y4C2 | protein_coding | deleterious(0.02) | probably_damaging(0.976) | TCGA-AP-A1DH-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TCAF1 | SNV | Missense_Mutation | novel | c.2701N>A | p.Ala901Thr | p.A901T | Q9Y4C2 | protein_coding | deleterious(0.04) | possibly_damaging(0.758) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 |
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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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