From: PheSeq, a Bayesian deep learning model to enhance and interpret the gene-disease association studies
Method | Data modality | Strategya | Interpretation | Countb | Hitc |
---|---|---|---|---|---|
Alzheimers’ disease | |||||
    Lee 22 [78] | GWAS + eQTL | Early | / | 12 | 8 |
    DeepGAMI [81] | Gene expression + GRN +eQTL | Early | Enrichment analysis | 102 | 2 |
    scGRNom [82] | GWAS + Hi-C | Intermediate | Enrichment analysis | 146 | 43 |
    GDAMDB [32] | GWAS \(+\) literature | Late | / | 149 | 72 |
    PheSeq | GWAS \(+\) literature \(+\) PPI | Late | Phenotype and literature | 1024 | 151 |
Breast cancer | |||||
    Kim 20 [79] | CNA + gene expression + methylations + clinical info | Intermediate | / | 36 | 5 |
    Ahn 14 [83] | Transcriptome + pathway | Early | / | 50 | 2 |
    GLRP [84] | Gene expression + PPI | Early | Interpretable neural network + pathway analysis | 167 | 5 |
    IMNA [85] | GWAS + eQTL | Early | Literature | 391 | 24 |
    PheSeq | Transcriptome \(+\) literature \(+\) PPI | Late | Phenotype and literature | 818 | 159 |
Lung cancer | |||||
    Zhang 20 [80] | Methylation + gene expression | Early | / | 23 | 2 |
    Gogleva 22 [86] | CRISPR + knowledge graph + literature | Intermediate | Interpretable recommendation system | 31 | 8 |
    CTpathway [87] | Gene expression + transcriptome + pathway + PPI | Intermediate | Pathway analysis | 59 | 12 |
    ECMarker [88] | Gene expression + clinical phenotype | Early | Interpretable neural network | 500 | 19 |
    PheSeq | Methylation \(+\) literature \(+\) PPI | Late | Phenotype and literature | 566 | 342 |