We just read a recent publication by Shankar et al that uses Avadis NGS to analyze RNA-Seq data. They study cells involved in rat placenta formation. The placenta is an organ that connects the foetus to the wall of the uterus, thus allowing for nutrients/oxygen to flow from mother to foetus, and waste to flow in the opposite direction. The rat placentation site is apparently made up of 3 very distinct functional areas. The goal of this study is to understand gene expression profiles in each of these 3 areas, and use these profiles to characterize the functions of each area. This paper shows that GO analysis on RNA-Seq data yields functions for each zone consistent with what is known (i.e., one zone specializes in transport of oxygen and nutrients, another drives the maternal hormonal response, and the third drives immune response). The paper then goes further to identify sets of transcription factors that are expressed differentially in each zone, and novel transcription factor networks (shown below, and created using the Avadis Protein-Protein Interactions Database) that may be at the heart of this differential behaviour.