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Table 3 Gene set enrichment analysis (GSEA) of genes differentially expressed in the acute phase only

From: T cell deficiency in spinal cord injury: altered locomotor recovery and whole-genome transcriptional analysis

Themea Gene set Genes % Acutely enriched −log(Q)b
AN (FC >1) SD (FC <1)
Immune system Cell adhesion molecules 25 32 68 Infinite
Cell surface interactions at the vascular wall 17 71 29 10.4
Hematopoietic cell lineage 14 64 36 7.6
Hemostasis 45 67 33 Infinite
Immune system 51 76 24 10.2
Leukocyte trans-endothelial migration 17 59 41 8.7
Platelet activation, signaling, and aggregation 21 62 38 8.1
Neurons and axons Axon guidance (Kegg gene set) 17 12 88 8.1
Axon guidance (Reactome gene set) 29 17 83 12.8
Neuroactive ligand-receptor interaction 23 22 78 7.6
Neuronal system 32 16 84 Infinite
Transmission across chemical synapses 24 17 83 11.5
GPCR signaling Class A1 rhodopsin-like receptors 24 46 54 7.3
GPCR ligand binding 32 41 59 9.9
GPCR signaling 45 42 58 7.6
Cell transport Solute carrier-mediated transmembrane transport 28 36 64 12.4
Transmembrane transport of small molecules 44 32 68 Infinite
Transport of inorganic cations/anions and amino acids/oligopeptides 19 32 68 12.4
Other Cell cycle 17 94 6 8.2
Developmental biology 32 22 78 10.2
  1. FC fold change (AN FKPM divided by SD FKPM), Q false discovery rate-adjusted P value
  2. aThe 20 most highly enriched gene sets have been manually grouped for conceptual purposes
  3. bThe value of −log(Q) is given for the GSEA Q value for each gene set