Examples

Configuring the DANSy workspace

For DANSy, we recommend having a whole proteome reference file within a central data directory that DANSy will use as a default reference file for any analysis. We provide an example that includes how to configure the workspace and create a reference file for the human protome using CoDIAC.

• Configuring your DANSy workspace

Base DANSy Analysis

In the base version of DANSy, a collection of proteins are analyzed. This creates a simple linguistic network class, which can be paired with existing network analysis tools (such as those found in the networkx package) to provide additional insights of abstract relationships between the functions of the proteins of interest. We have provided examples that demonstrate how to create the DANSy network for both a large and small collection of proteins.

• Base DANSy Analysis
• DANSy Analysis on a subset of proteins of interest
• Useful DANSy attributes and methods for additional analysis
• Generating a DANSy without the collapsing step

Differential Expression DANSy (deDANSy) Analysis

In deDANSy, the expression of each protein/gene is incorporated into the linguistic network and used to describe how distinct and separated functions endowed by the domains are for up- or down-regulated genes. In this analysis, we assume the expression status (i.e. up- vs down-regulated) is determined by both a combination of fold-change and statistical significance.

Important

This analysis can be conducted on either bulk RNA-sequencing or (phospho)proteomics datasets. We have not tested in other contexts, but if a set of gene IDs (e.g. ENSEMBL or Entrez IDs) or UniProt IDs are provided deDANSy can be potentially applied. However, we caution against using deDANSy for other applications currently.

Here, we provide example analyses that uses either RNA-sequencing results from Shimpi and Tan, et al, Adv Healthcare Mater (2021) or phosphoproteomic results from Chen, et al, Mol Cancer Ther (2024) to showcase the functionality of deDANSy.

• Performing deDANSy on an RNA-sequencing dataset (Shimpi & Tan et al. 2021)
  • Running additional comparisons after scores have been generated
• Determining the enriched n-grams of individual conditions.
• Performing deDANSy analysis with (phospho-)proteomic data