Figure 2 Selected GO terms related to “”GO: 0052040 modulation by symbiont of host programmed cell death”". A greatly simplified directed acyclic graph (DAG) showing key low-level terms describing modulation of programmed cell death
in one organism (the host) by another organism (the symbiont) is depicted. A simplified lineage for these terms is shown up to “”GO: 0008150 biological_process”". Only selected terms are shown, and only a few of the parent-child relationships are depicted; arrows symbolize GO “”is_a”" and “”part_of”" relationships (for more information on ontology structure, i.e. “”is_a”", “”part_of”", and “”regulates”", see [13]). Note that “”GO: 0052040 modulation by symbiont of host programmed cell death”" (denoted by a selleck dark SB203580 order star) and “”GO: 0052031 modulation by symbiont of host defense response”" (light star) both ultimately exist under the “”GO: 0051704 multi-organism process”" node. The GO terms shaded with grey represent annotations discussed in the text; GO terms highlighted with broken lines or black serve as reference points for Additional file1and Additional
file2, respectively. The term “”GO: 0052248 modulation of programmed cell death in other organism during symbiotic interaction”" can be viewed (highlighted in black) in Figure2, which depicts a greatly simplified directed acyclic graph (DAG; for more information on ontology structure see [13]) showing some more specific GO terms used to describe aspects of symbiont modulation of host programmed cell death. “”GO: 0052040 modulation by symbiont of host programmed cell death”" (shown in Figure2, denoted by a dark star), or a child term of this more general parent term if more specific annotation information
is available, would be used instead of “”GO: 0012501 Clomifene programmed cell death”" (Additional file1) to annotate any gene product produced by a symbiont that affected PCD in a host during a typical interaction. For example, the protein family, NPP1, comprises proteins from oomycetes, bacteria, and fungi that in plants cause HR-like cell death, pathogenesis-related gene transcription, reactive oxygen species (ROS) and ethylene (ET) generation, and apposition of callose, a (1→3)-β-d-glucan involved in both normal development and response to abiotic and biotic stress [31,32]. Annotating NPP1 family proteins with GO terms adds clarity not conferred by its literature description as a “”necrosis-inducing protein”". It would be appropriate to annotate aPhytophthora sojaemember of the family (e.g. PsojNIP; [33]) with the GO term “”GO: 0052040 modulation by symbiont of host programmed cell death”" (Figure2and Additional file2).