TL = tumor lysate sample
IF = interstitial fluid sample
Column explanation
IFgrTL
- Shows the result of a non-adjusted paired, two-sided t-test comparing matched TL and IF samples. If significant, this indicates that protein was identified in IF sample at higher levels than in TL sample. This may be beneficial for secreted biomarkers, as it may indicate particularly high levels of secretion.
TP53_OnOff
- Hand-curated list of proteins that were identified simply through the presence/absence in TP53 samples in IF dataset. Either direction, but looking for proteins that are high in one group (eg TP53 mut) and absent in other (TP53 nonmut)
TL_TP53_up
TL_TP53_down
- These are the results of the differential expression analysis comparing TP53 mutant vs nonmut TL samples
- To perform this comparison, a mixed imputation approach was used. This means that a different imputation was used for NA values that were assessed to be missing in a random pattern (this is common for proteomic datasets) than for those that were mostly missing from one of the two groups (TP53 mut vs non_mut)
- For a protein to be included in the MNAR group, all of the values in one of the groups need to be 0/NA with at most one exception. All other proteins with some NA values will be considered MAR.
- MAR (missing at random): for these proteins, NAs were imputed using a MLE approach within the DEP R package
- MNAR (missing not at random): for these proteins, NAs were imputed with zero within the DEP R package.
TL_TP53_params
- This is a more generous list for the TL_TP53 comparison (both up and down)
- Imputation strategy and some other parameters have very large effects on resulting lists of differentially expressed proteins. This is mostly due to the large number of NAs and the relatively small sample size. To ensure that important results were not missed, I performed the analysis with 360 different combinations of parameters, thus allowing me to identify proteins that are commonly captured in a subset of analyses
- This column includes all proteins identified in at least 10 of the 360 analyses
- This is a more generous list but treat with caution. Results should not be used for publication, only to help design follow up studies.
IF_TP53_up