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Gene: THRAP3 |
Gene summary for THRAP3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | THRAP3 | Gene ID | 9967 |
| Gene name | thyroid hormone receptor associated protein 3 | |
| Gene Alias | BCLAF2 | |
| Cytomap | 1p34.3 | |
| Gene Type | protein-coding | GO ID | GO:0000375 | UniProtAcc | Q9Y2W1 |
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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 |
| 9967 | THRAP3 | HTA11_347_2000001011 | Human | Colorectum | AD | 1.63e-08 | 5.73e-01 | -0.1954 |
| 9967 | THRAP3 | HTA11_411_2000001011 | Human | Colorectum | SER | 5.63e-03 | 7.64e-01 | -0.2602 |
| 9967 | THRAP3 | HTA11_1391_2000001011 | Human | Colorectum | AD | 2.00e-02 | 5.13e-01 | -0.059 |
| 9967 | THRAP3 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 1.56e-05 | 1.12e+00 | 0.3487 |
| 9967 | THRAP3 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 4.84e-03 | 5.39e-01 | 0.281 |
| 9967 | THRAP3 | A002-C-010 | Human | Colorectum | FAP | 1.92e-03 | -1.85e-01 | 0.242 |
| 9967 | THRAP3 | A015-C-203 | Human | Colorectum | FAP | 1.45e-23 | -3.12e-01 | -0.1294 |
| 9967 | THRAP3 | A015-C-204 | Human | Colorectum | FAP | 5.84e-04 | -1.95e-01 | -0.0228 |
| 9967 | THRAP3 | A014-C-040 | Human | Colorectum | FAP | 6.58e-04 | -3.19e-01 | -0.1184 |
| 9967 | THRAP3 | A002-C-201 | Human | Colorectum | FAP | 9.63e-11 | -3.15e-01 | 0.0324 |
| 9967 | THRAP3 | A002-C-203 | Human | Colorectum | FAP | 5.96e-07 | -1.87e-01 | 0.2786 |
| 9967 | THRAP3 | A001-C-119 | Human | Colorectum | FAP | 2.12e-03 | -4.78e-02 | -0.1557 |
| 9967 | THRAP3 | A001-C-108 | Human | Colorectum | FAP | 8.24e-14 | -1.66e-01 | -0.0272 |
| 9967 | THRAP3 | A002-C-205 | Human | Colorectum | FAP | 5.34e-18 | -2.18e-01 | -0.1236 |
| 9967 | THRAP3 | A001-C-104 | Human | Colorectum | FAP | 9.88e-03 | -8.36e-02 | 0.0184 |
| 9967 | THRAP3 | A015-C-005 | Human | Colorectum | FAP | 1.39e-02 | -2.04e-01 | -0.0336 |
| 9967 | THRAP3 | A015-C-006 | Human | Colorectum | FAP | 1.40e-12 | -7.38e-03 | -0.0994 |
| 9967 | THRAP3 | A015-C-106 | Human | Colorectum | FAP | 4.26e-11 | -1.84e-01 | -0.0511 |
| 9967 | THRAP3 | A002-C-114 | Human | Colorectum | FAP | 4.02e-14 | -2.71e-01 | -0.1561 |
| 9967 | THRAP3 | A015-C-104 | Human | Colorectum | FAP | 3.21e-22 | -1.45e-01 | -0.1899 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| 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 | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| 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 |
| 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:003312012 | Liver | HCC | positive regulation of RNA splicing | 29/7958 | 37/18723 | 9.37e-06 | 1.09e-04 | 29 |
| GO:00506851 | Liver | HCC | positive regulation of mRNA processing | 25/7958 | 32/18723 | 4.38e-05 | 4.26e-04 | 25 |
| GO:000762321 | Liver | HCC | circadian rhythm | 117/7958 | 210/18723 | 7.29e-05 | 6.54e-04 | 117 |
| GO:004851121 | Liver | HCC | rhythmic process | 156/7958 | 298/18723 | 3.54e-04 | 2.46e-03 | 156 |
| GO:190236921 | Liver | HCC | negative regulation of RNA catabolic process | 45/7958 | 75/18723 | 1.67e-03 | 8.73e-03 | 45 |
| GO:000038121 | Liver | HCC | regulation of alternative mRNA splicing, via spliceosome | 37/7958 | 60/18723 | 2.13e-03 | 1.07e-02 | 37 |
| GO:004348921 | Liver | HCC | RNA stabilization | 39/7958 | 65/18723 | 3.31e-03 | 1.51e-02 | 39 |
| GO:004802612 | Liver | HCC | positive regulation of mRNA splicing, via spliceosome | 16/7958 | 22/18723 | 4.03e-03 | 1.76e-02 | 16 |
| GO:190237311 | Liver | HCC | negative regulation of mRNA catabolic process | 37/7958 | 63/18723 | 6.82e-03 | 2.73e-02 | 37 |
| GO:004275211 | Liver | HCC | regulation of circadian rhythm | 65/7958 | 121/18723 | 8.25e-03 | 3.24e-02 | 65 |
| GO:004825511 | Liver | HCC | mRNA stabilization | 33/7958 | 56/18723 | 9.64e-03 | 3.63e-02 | 33 |
| GO:00434848 | Lung | IAC | regulation of RNA splicing | 49/2061 | 148/18723 | 4.76e-13 | 7.06e-10 | 49 |
| GO:19033117 | Lung | IAC | regulation of mRNA metabolic process | 71/2061 | 288/18723 | 3.76e-11 | 1.24e-08 | 71 |
| GO:00480248 | Lung | IAC | regulation of mRNA splicing, via spliceosome | 34/2061 | 101/18723 | 1.05e-09 | 1.95e-07 | 34 |
| GO:00506847 | Lung | IAC | regulation of mRNA processing | 41/2061 | 137/18723 | 1.23e-09 | 2.15e-07 | 41 |
| GO:00485116 | Lung | IAC | rhythmic process | 65/2061 | 298/18723 | 4.57e-08 | 5.02e-06 | 65 |
| GO:00098958 | Lung | IAC | negative regulation of catabolic process | 66/2061 | 320/18723 | 3.26e-07 | 2.48e-05 | 66 |
| GO:00313308 | Lung | IAC | negative regulation of cellular catabolic process | 57/2061 | 262/18723 | 3.31e-07 | 2.49e-05 | 57 |
| GO:00076237 | Lung | IAC | circadian rhythm | 48/2061 | 210/18723 | 6.13e-07 | 3.67e-05 | 48 |
| GO:00064027 | Lung | IAC | mRNA catabolic process | 50/2061 | 232/18723 | 2.28e-06 | 1.02e-04 | 50 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 |
| 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 |
| THRAP3 | SNV | Missense_Mutation | novel | c.953N>A | p.Gly318Asp | p.G318D | Q9Y2W1 | protein_coding | tolerated(0.22) | benign(0.215) | TCGA-A7-A6VX-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | docetaxel | CR |
| THRAP3 | SNV | Missense_Mutation | c.2428N>A | p.Asp810Asn | p.D810N | Q9Y2W1 | protein_coding | tolerated(0.69) | possibly_damaging(0.873) | TCGA-A8-A07B-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| THRAP3 | SNV | Missense_Mutation | c.869N>A | p.Gly290Asp | p.G290D | Q9Y2W1 | protein_coding | tolerated(0.07) | possibly_damaging(0.726) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| THRAP3 | SNV | Missense_Mutation | c.880N>G | p.Gln294Glu | p.Q294E | Q9Y2W1 | protein_coding | tolerated(0.12) | possibly_damaging(0.79) | TCGA-BH-A1EV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | |
| THRAP3 | SNV | Missense_Mutation | c.144N>C | p.Arg48Ser | p.R48S | Q9Y2W1 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.994) | TCGA-BH-A1FU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| THRAP3 | SNV | Missense_Mutation | rs749716914 | c.2080G>A | p.Asp694Asn | p.D694N | Q9Y2W1 | protein_coding | deleterious(0.02) | possibly_damaging(0.709) | TCGA-C8-A131-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | 5-fluorouracil | CR |
| THRAP3 | SNV | Missense_Mutation | c.2081A>T | p.Asp694Val | p.D694V | Q9Y2W1 | protein_coding | deleterious(0) | possibly_damaging(0.848) | TCGA-C8-A131-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | 5-fluorouracil | CR | |
| THRAP3 | SNV | Missense_Mutation | c.302N>C | p.Arg101Pro | p.R101P | Q9Y2W1 | protein_coding | deleterious(0.01) | probably_damaging(0.998) | TCGA-D8-A1XK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide | SD | |
| THRAP3 | SNV | Missense_Mutation | c.1403N>T | p.Ser468Leu | p.S468L | Q9Y2W1 | protein_coding | tolerated(0.67) | benign(0.15) | TCGA-E2-A9RU-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | arimidex | SD | |
| THRAP3 | SNV | Missense_Mutation | c.320A>C | p.Tyr107Ser | p.Y107S | Q9Y2W1 | protein_coding | deleterious(0.01) | probably_damaging(0.918) | TCGA-E9-A1N8-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
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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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