Fig. 1

Flowchart of the analysis pipeline which was applied to infer the autophagy PPI network in P. anserina. At the beginning of the pipeline, each autophagy-associated protein from yeast and human was identified. In parallel, a comprehensive BLAST search was applied, using the proteomes of P. anserina, yeast and human. Based on the initial protein set, the software package PATH2PPI was applied to find each interaction in the IREFINDEX database which is associated with autophagy in yeast and human. Subsequently, PATH2PPI used the sets of reference proteins, interactions and BLAST results to predict the putative autophagy PPI in P. anserina. To achieve the best possible prediction parameters, the prediction approach was repeated several times and each result was compared with the small, manually curated autophagy PPI network from KEGG. The best predicted PPI network was combined with the experimental results of a yeast two-hybrid analysis. Finally, the pipeline led to the autophagy PPI network in P. anserina which consists of 89 proteins and 186 interactions