This repo contains datasets and R scripts that were used to obtain the results described in the following study :
Cardiovirus leader proteins retarget RSK kinases toward alternative substrates to perturb nucleocytoplasmic traffic Belen Lizcano-Perret, Cecile Lardinois, Fanny Wavreil, Philippe Hauchamps, Gaetan Herinckx, Frederic Sorgeloos, Didier Vertommen, Laurent Gatto, Thomas Michiels bioRxiv 2022.06.16.496404; doi:10.1101/2022.06.16.496404
- Rmd scripts are stored in the main directory, together with html outputs.
- Dumps of intermediary R objects are stored in /rds directory. This allows to keep intermediary results in order to speed up the run of the script. However, if one would like to re-launch (parts of) the computations from scratch, one just need to delete (or rename) the corresponding .rds objects, and re-launch the .rmd scripts.
- Datasets are stored in /data directory. Additional information needed to interpret the datasets is provided herebelow.
MASSPROT experiment numbers:
- BioID-L: VIRO488 and VIRO523
- BioID-RSK: VIRO473 and VIRO523
| NI | WT (R02) | M60V (R02) | F48A | Replicate | |
|---|---|---|---|---|---|
| VIRO488_A3 | VIRO488_B3 | VIRO488_C3 | VIRO488_D3 | 1 | L |
| VIRO488_A2 | VIRO488_B2 | VIRO488_C2 | VIRO488_D2 | 1 | L |
| VIRO488_A1 | VIRO488_B1 | VIRO488_C1 | VIRO488_D1 | 1 | L |
| VIRO523_L1_01 | VIRO523_L1_02 | VIRO523_L1_03 | VIRO523_L1_04 | 2 | L |
| VIRO523_L1_05 | VIRO523_L1_06 | VIRO523_L1_07 | VIRO523_L1_08 | 2 | L |
| VIRO523_L1_09 | VIRO523_L1_10 | VIRO523_L1_11 | VIRO523_L1_12 | 2 | L |
| VIRO523_L2_01 | VIRO523_L2_02 | VIRO523_L2_03 | VIRO523_L2_04 | 3 | L |
| VIRO523_L2_05 | VIRO523_L2_06 | VIRO523_L2_07 | VIRO523_L2_08 | 3 | L |
| VIRO523_L2_09 | VIRO523_L2_10 | VIRO523_L2_11 | VIRO523_L2_12 | 3 | L |
| VIRO473_A3 | VIRO473_B3 | VIRO473_C3 | 1 | R | |
| VIRO473_A2 | VIRO473_B2 | VIRO473_C2 | 1 | R | |
| VIRO473_A1 | VIRO473_B1 | VIRO473_C1 | 1 | R | |
| VIRO523_R1_01 | VIRO523_R1_02 | VIRO523_R1_03 | 2 | R | |
| VIRO523_R1_04 | VIRO523_R1_05 | VIRO523_R1_06 | 2 | R | |
| VIRO523_R1_07 | VIRO523_R1_08 | VIRO523_R1_09 | 2 | R | |
| VIRO523_R2_01 | VIRO523_R2_02 | VIRO523_R2_03 | 3 | R | |
| VIRO523_R2_04 | VIRO523_R2_05 | VIRO523_R2_06 | 3 | R | |
| VIRO523_R2_07 | VIRO523_R2_08 | VIRO523_R2_09 | 3 | R |
- L-Experiment: MaxQuant analysis: 20191129 on windows computer: L: WT + M60V + F48A
- R-Experiment : MaxQuant analysis: 20191218 on windows computer : R : WT + M60V
Re-run from scratch of the computations with more recent versions of proDA might lead to slightly different outcomes (e.g. an impact on 4th digit - or further - on p-values has been seen), but should not change the conclusions of the analysis, i.e. order of differentially abundant proteins and shape of volcano plots.