Genome-wide analysis of primary peripheral blood mononuclear cells from HIV + patients-pre-and post- HAART show immune activation and inflammation the main drivers of host gene expression

Table 3 Generation of biological networks by MetaCore™ for the defense response for the disease section of the enrichment analysis

Key network objects	GO processes	p-Value
AKT(PKB), Caspase-9, HMGB1, Bcl-XL, IKK-beta	Regulation of defense response (74.0%), regulation of response to stress (80.0%), regulation of immune system process (82.0%), regulation of response to stimulus (92.0%), toll-like receptor 1 signaling pathway (40.0%)	1.31e-16
ATM, p21, MLL/MEN fusion protein, E1B-AP5, HEXIM1	Regulation of cell cycle (38.0%), cell cycle checkpoint (24.0%), chromatin organization (30.0%), negative regulation of cellular process (60.0%), chromatin modification (28.0%)	4.22e-39
CD19, CD79 complex, MHC class II, CD79B, IL-8	Immune response-regulating cell surface receptor signaling pathway (53.1%), positive regulation of T cell activation (55.1%), T cell co-stimulation (44.9%), lymphocyte co-stimulation (44.9%), response to interferon-gamma (49.0%)	1.82e-32
G3BP1 (hdhVIII), H-Ras, GPIAP1, ACSL3, IFNAR2	Leukocyte migration (46.0%), cell activation (54.0%), cell migration (52.0%), hemostasis (48.0%), localization of cell (52.0%)	2.05e-29
Casein kinase II, alpha chains, CD4, HSP27, IRF4, HDAC6	Regulation of macromolecule metabolic process (87.8%), regulation of primary metabolic process (87.8%), developmental process (87.8%), regulation of cellular metabolic process (87.8%), regulation of cellular biosynthetic process (79.6%)	1.40e-29

This is a variant of the shortest paths algorithm with main parameters of relative enrichment with the uploaded data and relative saturation of networks with canonical pathways. These networks are built on the fly and unique to the uploaded data. In this workflow the networks were prioritized based on the number of fragments of canonical pathways on the network.

ISSN: 2052-8426