Table 4:
Type and number of data modalities supported by each inter-modality data harmonization approach (restricted modality scope).
| Method name | No. of modalities compatible | 3D chromosome structure | DNA methylation | Epigenetic peak data | DNA-Protein binding | DNA-RNA interactions | RNA-Protein interactions | Protein-Protein interactions | Genomics | Transcriptomics | Citation |
|---|---|---|---|---|---|---|---|---|---|---|---|
| MDI | 3 | X | X | O | X | X | X | O | X | O | [49] |
| RIMBANET | 4 | X | X | X | O | X | X | O | O | O | [50] |
| EPIP | 4 | O | X | O | O | X | X | X | X | O | [44] |
| EAGLE | 2 | X | X | X | O | X | X | X | X | O | [51] |
| PreSTIGE | 2 | X | X | O | X | X | X | X | X | O | [52] |
| TEPIC | 3 | O | X | O | X | X | X | X | X | O | [45] |
| iOmicsPASS | 2 | X | X | X | X | X | X | X | O | O | [53] |
| LemonTree | 2 | X | X | X | X | X | X | X | O | O | [46] |
| PANDA | 3 | X | X | X | O | X | X | O | X | O | [54] |
| PARADIGM | 2 | X | X | X | X | X | X | X | O | O | [48] |
| IM-PET | 2 | X | X | O | X | X | X | X | X | O | [55] |
| JEME | 2 | X | X | O | X | X | X | X | X | O | [56] |
| RIPPLE | 3 | X | X | O | O | X | X | X | X | O | [57] |
| SVM-MAP | 2 | X | O | X | X | X | X | X | X | O | [58] |
| ELMER | 2 | X | O | X | X | X | X | X | X | O | [47] |
| TENET | 2 | X | O | X | X | X | X | X | X | O | [59] |
| RegNetDriver | 5 | X | O | O | O | X | X | X | O | O | [60] |
"DNA methylation" in this context refers specifically to the ratio of signal between methylated and unmethylated alleles. For simplicity, some modalities have been aggregated, e.g., transcriptomics data include both gene expression and small RNA data. Some methods are capable of handling proteomics, metabolomics, or medical images, but these are excluded because they are not a focus of this review. A link to each method is provided for easy reference.