Pathway, Molecular function, and Cellular compartment

By utilizing different tabs within the annotation tool, you can perform overrepresentation analyses and investigate various aspects of your data. Each tab — Pathways, Molecular functions, and Cellular compartments — provides unique insights, helping you to better understand the biological context and potential implications of your findings.

Below is a detailed guide on how to use each tab in the annotation tool.

💡 Good to know

The overrepresentation analysis does not reflect the whole dataset; as you have made a filtration of data, this should be considered when evaluating p-values and q-values.

Pathways

You are provided with an overrepresentation analysis from Reactome pathways based on the nodes (e.g, transcriptomics) in the chosen list.

The pathway annotation allows you to investigate which pathways your nodes could represent. This can provide answers to various questions. You may relate potential biomarkers to their system biological function and see if some of the pathways match your expectations. If you have included complete pathways for annotation, you may be investigating if daughter or parent pathways can be identified.

When exploring pathways, it can sometimes be observed that different parts of the pathway behave differently than others. Isolating the different parts of the pathways and testing if they are potential expressions of other pathways can be useful. The different parts can be sequentially annotated, and alternative pathways can be investigated.

Molecular functions

This tab offers an overrepresentation analysis from Gene Ontology's (GO) molecular functions database based on the nodes (e.g., proteomics) in the chosen list.

The molecular function annotation allows you to investigate which molecular functions your nodes (e.g., transcriptomics) are associated with. This can provide answers to various questions. You may relate potential biomarkers to their biological functions to see if they are important to the effects you observe. Alternatively, if you are looking for nodes with a specific function, the molecular function tab can be used to filter your list of potential candidates.

Cellular compartments

This tab provides an overrepresentation analysis from Gene Ontology's (GO) cellular compartment database based on the nodes (e.g., transcriptomics) in the chosen list.

The cellular compartment annotation allows you to investigate from which cellular compartment your transcripts/proteins are annotated. This can provide answers to various questions. For instance, you may want to specifically identify membrane or secreted proteins, as these could be easier to affect or detect using various workflows. Locations can also be important if you hypothesize that two proteins interact, as this would require them to be in proximity to each other.