Ranking and Filtering Differentially Abundant Proteins

Published

Jun 2026

This chapter turns a large differential result table into prioritized protein lists.

Core Outputs

all differential proteins
significant DEP
top upregulated proteins
top downregulated proteins
ranked protein list

Ranking Strategy

Proteins can be ranked by:

adjusted p-value
absolute log2 fold-change
direction of change
biological relevance
presence in known pathways or protein families

# Ranking and Filtering Differentially Abundant Proteins

This chapter turns a large differential result table into prioritized protein lists.

## Core Outputs

```text
all differential proteins
significant DEP
top upregulated proteins
top downregulated proteins
ranked protein list
```

## Ranking Strategy

Proteins can be ranked by:

- adjusted p-value
- absolute log2 fold-change
- direction of change
- biological relevance
- presence in known pathways or protein families