Table 2. Summary statistics for clusters of pathways enriched during FDMI and normal development.
Mean Normalised Enrichment Score (NES), false discovery rate (FDR) and signal strength statistic (Signal) for the biological pathways implicated by GSEA in control and FDM. Normal eye development implicated 10 cluster of pathways showing average signal strength while form-deprivation induction implicated 18 clusters of pathways. Pathways shown here only include clustered pathways as represented in Figs. 3 and 4 and do not include pathways that were unclustered. Further detail on the unclustered pathways can be found in File 1. The NES reflects the degree to which a set of genes is overrepresented at either the top or bottom of a ranked list of genes while also taking into account differences in pathway size (i.e., geneset size). NES is the primary statistic for examining enrichment results, and for comparing results across pathways. The percentage signal strength statistic reflects the proportion of the core set of genes that contribute most to a given pathway’s enrichment by accounting for particular genes position in the ranked list. A high signal strength indicates that the genes within a pathway are located close to the top (positive NES) or bottom (negative NES) of the ranked gene list. If the core genes are spread throughout the ranked list, then the signal strength decreases towards zero (Mootha et al., 2003; Subramanian et al., 2005).
| Cluster | Control | FDMI | ||||||
|---|---|---|---|---|---|---|---|---|
| Pathways in cluster | NES | FDR q-value | Signal | Pathways in cluster | NES | FDR q-value | Signal | |
| Cell cycle, mitotic | 5 | −2.233 | 0.019 | 31% | 3 | −2.253 | 0.009 | 98% |
| Cell maintenance & survival | – | – | – | – | 28 | −2.180 | 0.014 | 117% |
| Clatherin-mediated endocytosis (CME) | – | – | – | – | 2 | −2.014 | 0.032 | 81% |
| Complement and coagulation cascades (CCC) | – | – | – | – | 2 | 2.708 | 0.003 | 140% |
| Cytochrome p450 | 2 | 2.247 | 0.025 | 47% | 5 | 2.629 | 0.002 | 133% |
| Cytokine pathways | 2 | 2.717 | 0.002 | 40% | – | – | – | – |
| Neuron structure/growth | – | – | – | – | 5 | −2.321 | 0.007 | 80% |
| Fatty acid (FA) metabolism | – | – | – | – | 2 | −1.886 | 0.032 | 84% |
| Glucosaminoglycan (GAG) metabolism | 4 | 2.121 | 0.029 | 40% | – | – | – | – |
| Ion channel transport | – | – | – | – | 2 | −2.331 | 0.007 | 99% |
| Mitochondrial energy metabolism | – | – | – | – | 7 | 2.396 | 0.005 | 47% |
| Neurotransmission | 5 | −2.522 | 0.011 | 37% | 8 | −2.423 | 0.007 | 103% |
| Peroxisome | 2 | −2.221 | 0.017 | 40% | – | – | – | – |
| Phospholipid metabolism | 2 | −2.134 | 0.026 | 28% | 3 | −1.939 | 0.027 | 57% |
| Signal transduction, growth factors (GF) | – | – | – | – | 4 | −1.984 | 0.021 | 66% |
| Signal transduction, g-protein coupled receptors (GPCR) | 7 | 2.572 | 0.019 | 52% | 7 | 2.683 | 0.010 | 122% |
| Signal transduction, mitogen-activated protein kinases (MAPK) | – | – | – | – | 4 | −1.931 | 0.028 | 67% |
| Signal transduction, nerve growth factor (NGF) | – | – | – | – | 5 | −2.195 | 0.014 | 84% |
| Transcription | – | – | – | – | 10 | −2.218 | 0.013 | 120% |
| Translation | – | – | – | – | 8 | 2.731 | 0.001 | 46% |
| Ubiquitin-mediated proteolysis | 3 | −2.491 | 0.006 | 39% | – | – | – | – |
| Vesicle-mediated transport | 3 | −2.152 | 0.025 | 40% | 3 | −2.097 | 0.013 | 103% |