Hi Sam,

Even the fact that these terms are often used interchangeably, they refer to distinct aspects of proteomics data analysis.

Over-representation analysis is typically used to identify enriched functional categories or pathways within a set of proteins (i.e in GO enrichment analysis) while differential expression analysis (up- or down-regulation) is used to identify specific proteins that are differentially expressed between conditions.

I hope that this explanation helps.

Best,

Murat

I would extend that and say we really need to be careful using upregulated. To me, that means the expression of the protein is increased, so there is a fundamental change in the amount of protein quantified as a result of that. I'd suggest we use the term increased (or decreased) abundance when quantifying the protein, unless we have clear evidence to say otherwise. There are a lot of reasons protein quant differs between samples, and it's not always due to expression level changes. I agree you will find such terms used interchangeably, that does not mean it's correct, or a good idea.

Thank you Peter and Murat,

It makes sense actually that increased abundance refers to a single protein, whereas over-representation refers to a group of proteins.

I also tend associate upregulated and downregulated more with RNA than protein per se.