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The set of 28 genes was too small to identify statistically significant processes, however, the genes were mainly involved in metabolism and Pol II transcription.
GO analysis performed on the 146 genes showed that gene regulation was one of the top five statistically significant processes affected (Supplementary Table 6).
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Most of the statistically significant biological processes enriched in MP5 module can't go further than level 2 (i.e., cell cycle process and organelle organization), and therefore is expected a high <k> but lower k i m as shown in Table 3.
The top 30 most statistically significant GO Processes within induced genes were identified (Table 4).
Subsequently, the top 30 most statistically significant GO Processes from the top 750 induced and suppressed transcript sets were identified.
Similarly, the top 30 most statistically significant GO Processes within suppressed genes were also identified (Table 5).
No statistically significant biological processes resulted for miR-21 targets, most probably due to the highly stringent selection criteria of the algorithm used (see additional file 3).
As analysing these lists gene-by-gene is tedious and error prone, the genes in the lists are routinely annotated using Gene Ontology (GO) with an aim to identify statistically significant biological processes or pathways [ 1].
The interactive Web-based Ingenuity iReport program [ 12] based on Fisher's exact test (P-value < 0.01) was applied to identify the molecular functions of the products of the genes that exhibited altered expression in the conditions established, as well as signaling pathways and statistically significant biological processes.
For all statistically significant GO process terms, see Additional file 5.
Table 2 also lists statistically significant biological process GO terms associated with genes down-regulated during pregnancy.
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