Induced pluripotent stem (iPS) cells can be obtained from terminally 
differentiated somatic cells by overexpression of defined sets of reprogramming 
transcription factors. These protein sets have been called the Yamanaka factors, 
namely Sox2, Oct3/4 (Pou5f1), Klf4, and c-Myc, and the Thomson factors, namely 
Sox2, Oct3, Lin28, and Nanog. Other sets of proteins, while not essential for 
the formation of iPS cells, are important for improving the efficiency of the 
induction and still other sets of proteins are important as markers for 
embryonic stem cells. Structural information about most of these important 
proteins is very sparse. Our bioinformatics analysis herein reveals that these 
reprogramming factors and most of the efficiency-improving and embryonic stem 
cell markers are highly enriched in intrinsic disorder. As is typical for 
transcription factors, these proteins are modular. Specific sites for 
interaction with other proteins and DNA are dispersed in the long regions of 
intrinsic disorder. These highly dynamic interaction sites are evidently 
responsible for the delicate interplay among various molecules. The 
bioinformatics analysis given herein should facilitate the investigation of the 
roles and organization of these modular interaction sites, thereby helping to 
shed further light on the pathways that underlie the mechanism(s) by which 
terminally differentiated cells are converted to iPS cells.