Table 3.
Analysis of networks using MetaCore™. The gene content of the uploaded files was used as the input list for generating biological networks using the Analyze Networks (AN) algorithm with default settings. This is a variant of the shortest paths algorithm, with the following main parameters: (1) relative enrichment with the uploaded data and (2) relative saturation of networks with canonical pathways. These networks are built on the fly and are unique to the uploaded data. In this workflow, the networks are prioritized based on the number of fragments of canonical pathways in the network. S: size; T: target; P: pathways; G: gScore.
| No. | Processes | S | T | P | G |
|---|---|---|---|---|---|
| Common to All Four Networks | |||||
| 1 | Viral transcription (97.1%), viral genome expression (97.1%), translational termination (97.1%), cellular protein complex disassembly (97.1%), SRP (signal recognition particle)-dependent cotranslational protein targeting to membrane (97.1%). | 38 | 1 | 0 | 11.39 |
| Common to Two or Three of the Networks | |||||
| 1 | Positive regulation of nucleobase-containing compound metabolic process (75.5%), positive regulation of biosynthetic process (77.6%), enzyme-linked receptor protein signaling pathway (65.3%), positive regulation of nitrogen compound metabolic process (75.5%), positive regulation of macromolecule biosynthetic process (73.5%). | 50 | 16 | 0 | 69.15 |
| 2 | Positive regulation of response to stimulus (60.4%), regulation of response to stimulus (75.0%), response to organic substance (72.9%), transmembrane receptor protein tyrosine kinase signaling pathway (45.8%), response to hormone stimulus (56.2%). | 50 | 14 | 0 | 56.71 |
| 3 | Cell surface receptor signaling pathway (96.0%), signal transduction (96.0%), signaling (96.0%), single organism signaling (96.0%), cell communication (96.0%). | 50 | 2 | 30 | 45.94 |
| Unique to the 4 h Post-TBI Network | |||||
| 1 | Cell activation (54.0%), signal transduction (94.0%), signaling (96.0%), single organism signaling (96.0%), response to wounding (62.0%). | 50 | 6 | 0 | 43.25 |
| 2 | G-protein coupled receptor signaling pathway (71.4%), neuropeptide signaling pathway (30.6%), G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (32.7%), cell surface receptor signaling pathway (75.5%), chemokine-mediated signaling pathway (20.4%). | 50 | 5 | 0 | 36.02 |
| 3 | Axis specification (38.0%), canonical Wnt receptor signaling pathway (36.0%), pattern specification process (46.0%), Wnt receptor signaling pathway (38.0%), anterior/posterior pattern specification (36.0%). | 50 | 4 | 0 | 28.78 |
| Unique to the 8 h Post-TBI Network | |||||
| 1 | Response to abiotic stimulus (61.7%), regulation of apoptotic process (63.8%), regulation of programmed cell death (63.8%), positive regulation of cellular process (85.1%), positive regulation of metabolic process (74.5%). | 50 | 9 | 0 | 41.50 |
| 2 | Positive regulation of immune response (43.8%), positive regulation of response to stimulus (58.3%), regulation of response to stress (52.1%), regulation of immune response (47.9%), TRIF (Toll/IL-1 receptor domain-containing adapter inducing interferon-β)-dependent toll-like receptor signaling pathway (27.1%). | 50 | 8 | 0 | 36.87 |
| 3 | Immune response-activating signal transduction (25.0%), immune response-regulating signaling pathway (25.0%), T cell costimulation (17.5%), lymphocyte costimulation (17.5%), cellular defense response (17.5%). | 50 | 5 | 2 | 25.40 |
| Unique to the 24 h Post-TBI Network | |||||
| 1 | Double-strand break repair via synthesis-dependent strand annealing (100.0%), DNA recombinase assembly (100.0%), DNA excision (100.0%), telomere maintenance via semi-conservative replication (100.0%), nucleotide-excision repair, DNA gap filling (100.0%). | 4 | 2 | 0 | 33.30 |
| 2 | Lipoprotein metabolic process (46.2%), protein-lipid complex assembly (34.6%), plasma lipoprotein particle assembly (34.6%), lipid transport (50.0%), lipid localization (50.0%). | 49 | 6 | 0 | 30.34 |
| 3 | Immune response (56.5%), immune system process (67.4%), positive regulation of response to stimulus (58.7%), activation of immune response (39.1%), positive regulation of immune system process (47.8%). | 50 | 6 | 0 | 28.11 |
| Unique to the 72 h Post-TBI Network | |||||
| 1 | Positive regulation of biological process (98.0%), positive regulation of cellular process (90.0%), enzyme linked receptor protein signaling pathway (56.0%), regulation of immune system process (60.0%), regulation of response to stimulus (76.0%). | 50 | 13 | 0 | 65.57 |
| 2 | Positive regulation of apoptotic process (58.0%), positive regulation of programmed cell death (58.0%), positive regulation of cell death (58.0%), positive regulation of biological process (90.0%), regulation of apoptotic process (66.0%). | 50 | 11 | 0 | 55.45 |
| 3 | Enzyme linked receptor protein signaling pathway (63.8%), membrane protein intracellular domain proteolysis (25.5%), nerve growth factor receptor signaling pathway (40.4%), membrane protein proteolysis (25.5%), transmembrane receptor protein tyrosine kinase signaling pathway (46.8%). | 50 | 10 | 0 | 50.91 |