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 <codiac_>`_.

.. toctree::
   :maxdepth: 2
   
   setting_up_dansy.ipynb

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 <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.

.. toctree::
   :maxdepth: 2

   base_dansy.ipynb
   
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) <shimpi_data_>`_ or phosphoproteomic results from `Chen, et al, Mol Cancer Ther (2024) <chen_data_>`_ to showcase the functionality of deDANSy.

.. toctree::
   :maxdepth: 2

   deDANSy.ipynb


.. _networkx: https://networkx.org/
.. _shimpi_data: https://pmc.ncbi.nlm.nih.gov/articles/PMC10238572/
.. _chen_data: https://pmc.ncbi.nlm.nih.gov/articles/PMC10762338/
.. _codiac: https://github.com/NaegleLab/CoDIAC