Fig. 2.

Hierarchical organization of AIR. (A) The top phenotype layer contains immune cell types, cellular processes/phenotypes and tissue level organization. Clinicians are generally interested in connecting their patient data to this layer. (B) Each process in the top layer is connected to a respective signal flow diagram. The process layer describes key molecules/pathways regulating processes in the top layer. This layer is suitable for research scientists to generate new hypotheses on the mechanistic insights of disease phenotype regulation. (C) The lower layer contains a comprehensive Molecular Interaction Map (MIM) where all the processes are merged together at the molecular level. The layer is also enriched with currently available experimentally validated regulatory information. Each layer provides an opportunity to map and analyze specific data (e.g. Top layer: FACS analysis; middle layer: immune signaling; bottom layer: multi-omics data). Due to the communication across multiple layers, the AIR provides a platform to initiate integrative data analysis.