Tissue | Expression Dynamics | Abbreviation |
Colorectum (GSE201348) | ![The image shows the transcriptomic changes along malignancy continuum.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.](images/deg_images/Colorectum/Becker/TRIM28_pca_on_diff_genes.png) | FAP: Familial adenomatous polyposis |
CRC: Colorectal cancer |
Colorectum (HTA11) | ![The image shows the transcriptomic changes along malignancy continuum.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.](images/deg_images/Colorectum/Chen/TRIM28_pca_on_diff_genes.png) | AD: Adenomas |
SER: Sessile serrated lesions |
MSI-H: Microsatellite-high colorectal cancer |
MSS: Microsatellite stable colorectal cancer |
Endometrium | ![The image shows the transcriptomic changes along malignancy continuum.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.](images/deg_images/Endometrium/TRIM28_pca_on_diff_genes.png) | AEH: Atypical endometrial hyperplasia |
EEC: Endometrioid Cancer |
Esophagus | ![The image shows the transcriptomic changes along malignancy continuum.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.](images/deg_images/Esophagus/TRIM28_pca_on_diff_genes.png) | ESCC: Esophageal squamous cell carcinoma |
HGIN: High-grade intraepithelial neoplasias |
LGIN: Low-grade intraepithelial neoplasias |
Liver | ![The image shows the transcriptomic changes along malignancy continuum.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.](images/deg_images/Liver/TRIM28_pca_on_diff_genes.png) | HCC: Hepatocellular carcinoma |
NAFLD: Non-alcoholic fatty liver disease |
Lung | ![The image shows the transcriptomic changes along malignancy continuum.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.](images/deg_images/Lung/TRIM28_pca_on_diff_genes.png) | AAH: Atypical adenomatous hyperplasia |
AIS: Adenocarcinoma in situ |
IAC: Invasive lung adenocarcinoma |
MIA: Minimally invasive adenocarcinoma |
Oral Cavity | ![The image shows the transcriptomic changes along malignancy continuum.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.](images/deg_images/OralCavity/TRIM28_pca_on_diff_genes.png) | EOLP: Erosive Oral lichen planus |
LP: leukoplakia |
NEOLP: Non-erosive oral lichen planus |
OSCC: Oral squamous cell carcinoma |
Skin | ![The image shows the transcriptomic changes along malignancy continuum.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.](images/deg_images/Skin/TRIM28_pca_on_diff_genes.png) | AK: Actinic keratosis |
cSCC: Cutaneous squamous cell carcinoma |
SCCIS:squamous cell carcinoma in situ |
Thyroid | ![The image shows the transcriptomic changes along malignancy continuum.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.](images/deg_images/Thyroid/TRIM28_pca_on_diff_genes.png) | ATC: Anaplastic thyroid cancer |
HT: Hashimoto's thyroiditis |
PTC: Papillary thyroid cancer |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:000628211 | Thyroid | ATC | regulation of DNA repair | 68/6293 | 130/18723 | 8.19e-06 | 8.27e-05 | 68 |
GO:004002913 | Thyroid | ATC | regulation of gene expression, epigenetic | 57/6293 | 105/18723 | 1.01e-05 | 1.00e-04 | 57 |
GO:000189026 | Thyroid | ATC | placenta development | 70/6293 | 144/18723 | 1.33e-04 | 9.33e-04 | 70 |
GO:001692513 | Thyroid | ATC | protein sumoylation | 30/6293 | 53/18723 | 4.84e-04 | 2.83e-03 | 30 |
GO:0001892111 | Thyroid | ATC | embryonic placenta development | 42/6293 | 82/18723 | 7.34e-04 | 4.11e-03 | 42 |
GO:004338832 | Thyroid | ATC | positive regulation of DNA binding | 30/6293 | 56/18723 | 1.63e-03 | 8.18e-03 | 30 |
GO:004573911 | Thyroid | ATC | positive regulation of DNA repair | 37/6293 | 73/18723 | 1.89e-03 | 9.24e-03 | 37 |
GO:004341412 | Thyroid | ATC | macromolecule methylation | 131/6293 | 316/18723 | 2.01e-03 | 9.60e-03 | 131 |
GO:00485688 | Thyroid | ATC | embryonic organ development | 172/6293 | 427/18723 | 2.08e-03 | 9.84e-03 | 172 |
GO:001907621 | Thyroid | ATC | viral release from host cell | 20/6293 | 34/18723 | 2.22e-03 | 1.04e-02 | 20 |
GO:003589021 | Thyroid | ATC | exit from host | 20/6293 | 34/18723 | 2.22e-03 | 1.04e-02 | 20 |
GO:003589121 | Thyroid | ATC | exit from host cell | 20/6293 | 34/18723 | 2.22e-03 | 1.04e-02 | 20 |
GO:00458141 | Thyroid | ATC | negative regulation of gene expression, epigenetic | 27/6293 | 50/18723 | 2.35e-03 | 1.10e-02 | 27 |
GO:003225911 | Thyroid | ATC | methylation | 148/6293 | 364/18723 | 2.69e-03 | 1.23e-02 | 148 |
GO:00315071 | Thyroid | ATC | heterochromatin assembly | 22/6293 | 39/18723 | 2.84e-03 | 1.29e-02 | 22 |
GO:004390327 | Thyroid | ATC | regulation of biological process involved in symbiotic interaction | 36/6293 | 72/18723 | 2.91e-03 | 1.32e-02 | 36 |
GO:007082811 | Thyroid | ATC | heterochromatin organization | 25/6293 | 46/18723 | 3.00e-03 | 1.36e-02 | 25 |
GO:00510531 | Thyroid | ATC | negative regulation of DNA metabolic process | 57/6293 | 125/18723 | 3.47e-03 | 1.55e-02 | 57 |
GO:004507110 | Thyroid | ATC | negative regulation of viral genome replication | 29/6293 | 56/18723 | 3.76e-03 | 1.64e-02 | 29 |
GO:004852518 | Thyroid | ATC | negative regulation of viral process | 43/6293 | 92/18723 | 6.02e-03 | 2.42e-02 | 43 |
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 |
TRIM28 | SNV | Missense_Mutation | novel | c.523G>A | p.Glu175Lys | p.E175K | Q13263 | protein_coding | deleterious(0.04) | benign(0.286) | TCGA-A2-A0CR-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
TRIM28 | SNV | Missense_Mutation | rs759243122 | c.1234N>T | p.Arg412Cys | p.R412C | Q13263 | protein_coding | tolerated(0.06) | probably_damaging(0.99) | TCGA-AO-A0J3-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | cyclophosphamide | SD |
TRIM28 | SNV | Missense_Mutation | | c.932G>A | p.Arg311His | p.R311H | Q13263 | protein_coding | tolerated(0.1) | benign(0.003) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
TRIM28 | SNV | Missense_Mutation | | c.1310N>G | p.Ser437Cys | p.S437C | Q13263 | protein_coding | deleterious(0.01) | possibly_damaging(0.635) | TCGA-BH-A0DZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | docetaxel | SD |
TRIM28 | SNV | Missense_Mutation | novel | c.667N>G | p.Ser223Gly | p.S223G | Q13263 | protein_coding | deleterious(0) | possibly_damaging(0.867) | TCGA-EW-A1OY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
TRIM28 | deletion | Frame_Shift_Del | novel | c.479delN | p.Pro161GlnfsTer18 | p.P161Qfs*18 | Q13263 | protein_coding | | | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
TRIM28 | deletion | Frame_Shift_Del | novel | c.2049delN | p.Leu684TrpfsTer57 | p.L684Wfs*57 | Q13263 | protein_coding | | | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD |
TRIM28 | SNV | Missense_Mutation | novel | c.1486N>A | p.Asp496Asn | p.D496N | Q13263 | protein_coding | tolerated(0.82) | probably_damaging(0.977) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
TRIM28 | SNV | Missense_Mutation | novel | c.2377G>A | p.Glu793Lys | p.E793K | Q13263 | protein_coding | deleterious(0.03) | benign(0.014) | TCGA-C5-A7X5-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | carboplatin | PD |
TRIM28 | SNV | Missense_Mutation | novel | c.736N>C | p.Glu246Gln | p.E246Q | Q13263 | protein_coding | deleterious(0.02) | probably_damaging(0.991) | TCGA-DS-A1OC-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | gemcitabine | SD |