Biological Interpretation of Omics Data

Having identified and quantified gene or protein expression across biological samples, what do these results mean in terms of the underlying biology? See refs on zotero here

Questions that can be addressed include:

• What biological pathways or processes are perturbed in my samples?
• Are there specific classes of protein, in terms of their function that are enriched in my data?
• Do my data suggest new interactions between proteins or support known protein complexes?

To address these questions, we can use several different online tools. The analysis of sets of proteins identified by proteomics experiments is very similar in concept to analysis of sets of perturbed genes in gene-expression experiments, or indeed the output of other 'omics techniques. The tools we use therefore are general purpose 'omics data analysis tools.

Analyzing annotation trends using the Gene Ontology

There are many tools that calculate the significance of annotation trends - essentially the probability of observing the given number of genes belonging to a given class (function, pathway, process etc). In this tutorial, we make use of the Gene Ontology, and 2 different and convenient tools for displaying those Gene Ontology categories that are significantly over- or under-represented in the proteomics (or transcriptomics) data.

	To find significant functions or pathways in our query data, we compare the query of genes to a 'background' set, typically the complete set of genes from the organism. Download complete lists of human and mouse gene symbols. Choose organism Choose the Two unranked lists of genes option Choose ontology=all and search
	Paste in your gene symbols and submit Select the ontologies tab to see the Gene Ontology enrichment

Analyzing functional molecular networks using STRING

Select multiple names tab for analysis of list Select organism or auto-detect

Other network and annotation analysis tools

• Toppgene functional analysis tool
• DAVID tools at NCBI
• Gene Mania tool for functional network analysis
• Ingenuity pathways analysis provides similar functionality, and also enables the analysis of lists of proteins (license required).
• Neat 3D interaction network visualisation
• Cytoscape is an excellent tool for visualizing interaction networks with many online tutorials.
  1. File->Import->Import Network from Web Services (retrieve pathways).
  2. Insert your favourite gene (APC, MRE11 ...) and select the pathways or networks.
  3. Re-arrange the network (Layout menu).
  4. Change the node and edge attributes