Table 3 Associated phenotypes for PheSeq recalled genes
From: PheSeq, a Bayesian deep learning model to enhance and interpret the gene-disease association studies
Gene | Significant in PheSeq | Significant in SAa | # of phenotype | Phenotype ID | Phenotype term | # of citation |
|---|---|---|---|---|---|---|
Alzheimer’s disease | ||||||
    MAPT | Strict | Less | 118 | HP:0002185 | Neurofibrillary tangles | 202 |
GO:0048151 | Hyperphosphorylation | 105 | ||||
HP:0100543 | Cognitive impairment | 69 | ||||
GO:0008017 | Microtubule binding | 24 | ||||
GO:0060291 | Long-term synaptic potentiation | 21 | ||||
GO:0046785 | Microtubule polymerization potentiation | 15 | ||||
    PSEN1 | Strict | Less | 121 | HP:0011034 | Amyloidosis | 102 |
GO:0016310 | Phosphorylation | 55 | ||||
GO:0016236 | Macroautophagy | 51 | ||||
GO:0060291 | Long-term synaptic potentiation | 32 | ||||
HP:0002185 | Neurofibrillary tangles | 21 | ||||
HP:0100256 | Senile plaques | 19 | ||||
    C9orf72 | Strict | Limited | 128 | GO:0008384 | IkappaB kinase activity | 26 |
GO:0004784 | Superoxide dismutase activity | 17 | ||||
GO:0003777 | Microtubule motor activity | 14 | ||||
HP:0410170 | Hippocampal atrophy | 13 | ||||
HP:0007112 | Temporal cortical atrophy | 11 | ||||
HP:0002354 | Memory impairment | 6 | ||||
    SOD1 | Strict | Less | 84 | GO:0004784 | Superoxide dismutase activity | 153 |
HP:0007373 | Motor neuron atrophy | 48 | ||||
HP:0003287 | Abnormality of mitochondrial metabolism | 20 | ||||
GO:0000422 | Autophagy of mitochondria | 19 | ||||
GO:0003777 | Microtubule motor activity | 15 | ||||
    PSEN2 | Strict | Less | 84 | GO:0042982 | Amyloid precursor protein metabolic process | 88 |
GO:0006954 | Inflammatory response | 78 | ||||
HP:0100256 | Senile plaques | 73 | ||||
GO:0060291 | Long-term synaptic potentiation | 65 | ||||
HP:0002529 | Neuronal loss in central nervous system | 32 | ||||
Breast cancer | ||||||
    NEU1 | Strict | Less | 67 | GO:0001525 | Angiogenesis | 87 |
GO:0001837 | Epithelial to mesenchymal transition | 77 | ||||
GO:0006915 | Apoptotic process | 43 | ||||
GO:0007155 | Cell adhesion | 26 | ||||
GO:0012501 | Programmed cell death | 24 | ||||
    ZAP70 | Strict | Limited | 74 | GO:0001816 | Cytokine production | 146 |
GO:0002870 | T cell anergy | 78 | ||||
GO:0012501 | Programmed cell death | 43 | ||||
GO:0008283 | Cell population proliferation | 24 | ||||
GO:0042110 | T cell activation | 24 | ||||
    EIF2S2 | Strict | Less | 34 | GO:0004030 | Aldehyde dehydrogenase [NAD(P)+] activity | 155 |
GO:0007049 | Cell cycle | 112 | ||||
GO:0042571 | Immunoglobulin complex, circulating | 56 | ||||
GO:0019815 | B Cell receptor complex | 46 | ||||
GO:0005850 | Eukaryotic translation initiation factor 2 complex | 43 | ||||
    ZNRF3 | Strict | Limited | 32 | GO:0001837 | Epithelial to mesenchymal transition | 96 |
GO:0004693 | Cyclin-dependent protein serine/threonine kinase activity | 38 | ||||
GO:0016055 | Wnt signaling pathway | 37 | ||||
GO:0044214 | Spanning component of plasma membrane | 32 | ||||
GO:0008283 | Cell population proliferation | 12 | ||||
    CLIC1 | Strict | Less | 57 | GO:0005161 | Platelet-derived growth factor receptor binding | 53 |
GO:0001837 | Epithelial to mesenchymal transition | 38 | ||||
GO:0005006 | Epidermal growth factor-activated receptor activity | 51 | ||||
GO:0005104 | Fibroblast growth factor receptor binding | 37 | ||||
GO:0005172 | Vascular endothelial growth factor receptor binding | 31 | ||||
Lung Cancer | ||||||
    UGT2B15 | Strict | Limited | 63 | GO:0004707 | MAP kinase activity | 155 |
GO:0005041 | Low-density lipoprotein particle receptor activity | 91 | ||||
GO:0005007 | Fibroblast growth factor-activated receptor activity | 82 | ||||
GO:0005104 | Fibroblast growth factor receptor binding | 82 | ||||
GO:0005172 | Vascular endothelial growth factor receptor binding | 65 | ||||
    VPS33B | Strict | Limited | 30 | GO:0001837 | Epithelial to mesenchymal transition | 147 |
GO:0005006 | Epidermal growth factor-activated receptor activity | 51 | ||||
GO:0016192 | Vesicle-mediated transport | 42 | ||||
HP:0100630 | Nasopharyngeal | 39 | ||||
GO:0005092 | GDP-dissociation inhibitor activity | 12 | ||||
    ATAD5 | Strict | Limited | 29 | GO:0072671 | Mito-associated ubiquitin-dependent protein catabolic process | 50 |
GO:0005007 | Fibroblast growth factor-activated receptor activity | 47 | ||||
GO:0005011 | Macrophage colony-stimulating factor receptor activity | 45 | ||||
GO:0008384 | IkappaB kinase activity | 31 | ||||
GO:0033868 | Goodpasture-antigen-binding protein kinase activity | 21 | ||||
    GNAT2 | Strict | Limited | 28 | GO:0005680 | Anaphase-promoting complex | 111 |
GO:0001532 | Interleukin-21 receptor activity | 67 | ||||
GO:0033868 | Goodpasture-antigen-binding protein kinase activity | 63 | ||||
GO:0072671 | Mito-associated ubiquitin-dependent protein catabolic process | 54 | ||||
GO:0004709 | MAP kinase activity tangles | 21 | ||||
    SPPL3 | Strict | Limited | 28 | GO:0001837 | Epithelial to mesenchymal transition | 76 |
GO:0005104 | Fibroblast growth factor receptor binding | 65 | ||||
GO:0005149 | Interleukin-1 receptor binding | 32 | ||||
GO:0005160 | Transforming growth factor beta receptor binding | 26 | ||||
GO:0005164 | Tumor necrosis factor receptor binding | 12 | ||||