Supplemental materials for preprint: Better than flipping a coin? Organ specific plasma proteins are not confidently identified by gene expression data

Supplemental Information for
Organ specific proteins are not confidently identified by gene expression data
Benjamin Orsburn
Summary of these materials
Supplemental 1 "Oh et al., Organ Specific"
Oh et al., list of organ specific targets
Organ aging signatures in the plasma proteome track health and disease
https://www.nature.com/articles/s41586-023-06802-1
Supplemental
2 "15,210 proteins in 29 organs"
A table of 15,210 proteins from Wang et al.,
A deep proteome and transcriptome abundance atlas of 29 healthy human tissues
https://www.embopress.org/doi/full/10.15252/msb.20188503
Supplemental 3 "How to spotcheck proteins"
A short walkthrough and some example results of how to spotcheck proteins against http://www.humanproteomemap.org/
As detailed in Kim et al. A draft map of the human proteome. 2014. Nature. 509, 575-581
Supplemental 4 "Combined Analysis"
Targets between Oh et al., and Wang et al., that can be directly matched.
To perform this analysis, I used the Excel "XLOOKUP" function to pull the proteins and their abundance from Sheet 2 which were listed as organ specific in Sheet 1
The resulting proteins were then sorted by GTEX organ as in sheet 1
Two analyses were performed on the 460 proteins that could be matched at a protein and organ level.
Analysis 1: Repeat of Oh et al., assumption.
Is the protein 4x or more abundant in the organ in question compared to the other 15 organs where we have overlap?
This was performed by a simple IF, THEN argument (
Results in Column AP, with final sums in AP681 and AP682
Analysis 2:
Is the abundance of this protein expression higher than the sum of the abundance of this protein in the other 15 organs where we have overlap?
This was again a simple IF, THEN argument
Results are in Column AK, with final sums in AK681 and AK682