Table 4.
Kinase activity prediction and phosphoproteomic dataset analysis tools
| Tool | Last update | Prediction type | Method | Input | Type | References |
|---|---|---|---|---|---|---|
| PHOSIDA Motif Finder | 2011 | Sequence motifs | Bootstrap | Phosphosite 13mer | Web | [26] |
| CellNOpt | 2012 | Time-course analysis | Logic formalisms | Interactions and phosphoproteomic data | Tool | [85] |
| KEA2 | 2012 | Kinase activity | Fisher’s exact test | Gene symbols and phosphosite | Web|DL|Tool | [74] |
| Sorad | 2013 | Time-course analysis | Ordinary differential equations | Phosphoproteomic data | Tool | [86] |
| PHOXTRACK | 2014 | Kinase activity | GSEA | Phosphosite 13mer and log2 expression | Web|DL | [75] |
| PhosFox | 2015 | Phosphorylation site comparison between groups | Comparison | Phosphoproteomic data | Tool | [84] |
| SELPHI | 2015 | Phosphoproteomic data analysis | Multiple functions | Phosphoproteomic data | Web|DL | [83] |
| DynaPho | 2016 | Phosphoproteomic analysis for multiple conditions | Activity modules | phosphoproteomic data | Web|DL | [87] |
| IKAP | 2016 | Kinase activity | Cost function | Phosphoproteomic data | Tool | [76] |
| KinasePA | 2016 | Kinase perturbation in multiple treatments | Directional hypothesis testing framework | Phosphoproteomic data | Web|Tool | [88] |
| KSEA | 2017 | Kinase activity | Z score | Phosphoproteomic data | Web|DL|Tool | [4] |
| CLUE | 2018 | Time-course kinase activity | k-Means clustering | Phosphoproteomic data | Tool | [41] |
| INKA | 2019 | Kinase activity | GSEA and phosphorylation | Phosphoproteomic data | Web|DL | [77] |
GSEA gene set enrichment analysis