Fig. 3

Gene set enrichment analysis (GSEA) identifies miR-27b-regulated gene networks associated with neurotransmission and cell proliferation. a-d GSEA analysis of the microarray data. Out of a total of 1330 gene sets, 63 were significantly enriched at the top and 113 were significantly enriched at the bottom of the gene ranked list (See Additional files 6 and 7: Tables S5,S6). a,c Selected down- and up-regulated gene sets linked to neurotransmission (a) and cell proliferation (c). Gene sets are ranked according to their normalized enrichment score (NES). The false discovery rate (FDR) is the estimated probability that a gene set with a given NES represents a false-positive. K (KEGG) and R (Reactome) indicate the source of pathways. b,d Enrichment score (ES) plots for the indicated gene sets. Negative and positive ES values point to gene sets over-represented in the top most down- or up-regulated genes in miR-27b KD neurons. Vertical bars refer to individual genes in a gene set and their position reflects the contribution of each gene to the ES. Genes that belong to the leading edge subset (i.e. genes that appear at or after the ES minimum (b) and at or before the ES maximum (d)) contribute to the enrichment signal. e Network analysis of gene sets. Shown are the two largest networks of down-regulated (blue) and up-regulated (red) gene sets. They are comprised of gene sets listed in (a) and (c) (see Additional file 8: Figure S2 for the visualization of all detected networks). Node size is proportional to the number of genes in the microarray that are represented in the gene set. Color intensity of the node (light to dark) indicates the significance of the gene set. Edge size corresponds to the number of genes that overlap between two connected gene sets. f,g Hierarchical clustering of differentially-expressed genes belonging to the leading edge subset of the indicated gene sets. Rows indicate individual miR-27b CT and KD conditions. f Genes with clear roles in pre- or post-synaptic functions are indicated