Threshold selection in gene co-expression networks using spectral graph theory techniques

Table 4 IPA networks from two paracliques

IPA networks
Paraclique	Threshold	Unique genes	Network functions
1	0.65	21	Hematological System Development and Function, Humoral Immune Response, Tissue Morphology Cellular Movement, Embryonic Development, Hair and Skin Development and Function
2	0.83	13	Hematological System Development and Function, Humoral Immune Response, Tissue Morphology Cellular Movement, Embryonic Development, Hair and Skin Development and Function

Paraclique 1 was extracted from a graph constructed at the 0.65 threshold while the smaller paraclique 2 is from a graph at the 0.83 threshold level. IPA indicates that genes from both of these gene sets match a similar set of network functions. In both cases, the set of focus molecules identified by IPA consisted of IGHD, IGHG1, IGHM, IGKC, and IGL for the first network and IGKV1–5 for the second.