The RIKEN mouse transcriptome: lessons learned and implications for the regulation of immune reactions.

Notably, the technology and analysis methods of the RIKEN mouse full-length cDNA project have contributed a lot to the capture of the transcriptional output of the mouse genome and the description of its combinatorial nature. However, one corollary of this large scale transcript resource is the dichotomy of vast and missing information. As such, the transcriptional and translational output of yet unknown size following non-canonical principles remains to be established and interpreted. The importance of identifying immune-related transcripts and establishing their molecular functions in context of complex immune system diseases is clear: knowledge about the transcriptome can advance the understanding of immune system regulation. Decipher ing the logic of transcriptomes is critical for understanding the ontogeny and effector functions of immune cells, but it is not sufficient. The next challenge will lie in the combined sampling and integrated analysis of genomic elements, transcripts, proteins and metabolites.