ANAT - Advanced Network Analysis Tool An interactive system for inference and analysis of functional networks of proteins.

Generating the Autophagy-apoptosis Network

We demonstrate the utility of ANAT by studying the cross talk between the autophagic and apoptotic cell death modules in human using a network of physical interactions. The construction of the network and the ensuing analysis were described in the manuscript.

  • The input files for generating the autophagy-apoptosis cross talk network (Figures 2, 4, 5) may be downloaded here.
  • The generated HTML reports, providing the functional enrichment analysis may be downloaded here.
  • The list of constraints, added while constructing the network may be downloaded here.
  • Note that due to ongoing updates to ANAT's networks, your results will differ from those seen in the manuscript.

Generating the Result Network (Figure 2)

The resulting network may be downloaded here. The following steps may be used to generate it using ANAT:

  1. Click the “New subnetwork” button in the ANAT tab.
  2. Fill in a meaningful name in the title field. For example: "Autophagy-apoptosis case study".
  3. Make sure the “Anchored networks” algorithm is selected.
  4. From the list of networks, select H_Sapiens.
  5. Click on the “Advanced” button
  6. In the “Modify base network” section, click "Import" and upload the file "ANAT_PCD_bckground.xml".
  7. In the following window "Anchored networks parameters" click "Import" and choose the file "input.xml".
  8. Click “Finish”.

* To view the enrichment analysis of the pathways in the resulting autophagy-apoptosis cross talk network, click the “Open HTML report” button that is placed on the bottom of ANAT panel.

Generating the Alternative Models (Figure 5)

Follow these steps:

  1. Click the “Modify Parameters" and the click "Advanced".
  2. To generate the model in Figure 5A, check the "Enable node penalty" box.
  3. To generate the model in Figure 5B, enter 1 in the "Margin" text box.
  4. Click “Finish”.