Table 2.

Functional analysis of mRNAs within the miRNA-TF-TG closed loop-motifs at 24h and 7d

Biological process	Time point	Enrichment score	P-value	Closed loop-motifs
Cell death**	Early (24 h)	≥2.79	≤1.7E-3	1047
Ion transport*		2.13	7.3E-5	367
Synaptic activity**		≥1.1	≤7.7E-1	285
Apoptosis*		2.95	1.0E-3	144
Caspase activity*		1.74	1.5E-2	39
		Total loop-motifs 24h		1278
Cell death**	Late (7d)	≥2.7	≤2.3E-3	316
Antigen presentation**		≥4.11	≤3.8E-9	113
Ion transport**		≥2.67	≤1.1E-4	100
Immune response *		8.1	5.8E-12	98
Inflammatory response*		11.41	2.6E-9	45
		Total loop-motifs 7d		413

*Biological processes based on analyses by DAVID.

**Biological processes based on combined analyses by DAVID and IPA. In the combined analyses we summed the genes assigned by DAVID and IPA to the same biological process. The enrichment scores and p-values were obtained from either DAVID or IPA based on which of them provided the lowest p-values and the highest enrichment scores.

The mRNAs in the TF-mRNA and miRNA-mRNA pairs were analyzed with the aid of DAVID and IPA to find the biological processes affected by the IR-injury. The top biological process terms were identified by combining results from DAVID and IPA. DAVID and IPA provided the enrichment scores and their associated p-values. The numbers of closed loop-motifs for each biological process were then based on the mRNAs associated with each process. Note: there are closed loop-motifs that are shared among the biological processes and this reflects their total numbers (see Figures 5 and 7). All loop-motifs are part of the larger regulatory networks seen in Figure 3.