BMC Neuroscience

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

Theme^a	Gene set	Genes	% Acutely enriched		−log(Q)^b
Theme^a	Gene set	Genes	AN (FC >1)	SD (FC <1)	−log(Q)^b
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
Other	Developmental biology	32	22	78	10.2

FC fold change (AN FKPM divided by SD FKPM), Q false discovery rate-adjusted P value
^aThe 20 most highly enriched gene sets have been manually grouped for conceptual purposes
^bThe value of −log(Q) is given for the GSEA Q value for each gene set

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ISSN: 1471-2202

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