Summary of categories of biological processes that are significantly overrepresented by genes misregulated in NS knockdown cells (with at least fourfold change and adjusted P-value < 0.05) when compared with controls with scrambled shRNA (Ctl)
| NS KD vs. Ctl ESCs | Biological Process | Count | Expected Count | P-value |
| Down-regulated | Glycolysis | 4 | 0.2 | 8.07E–03 |
| Chromosome segregation | 5 | 0.41 | 1.21E–02 | |
| Cell cycle | 11 | 3.49 | 2.40E–02 | |
| Developmental processes | 18 | 8.29 | 4.42E–02 | |
| Up-regulated | Developmental processes | 60 | 20.25 | 6.30E–13 |
| Cell structure and motility | 33 | 9.58 | 2.67E–08 | |
| Cell structure | 25 | 5.76 | 1.83E–07 | |
| Mesoderm development | 20 | 4.89 | 2.28E–05 | |
| mRNA transcription regulation | 36 | 14.32 | 7.97E–05 | |
| Cell communication | 29 | 10.67 | 1.94E–04 | |
| Embryogenesis | 10 | 1.42 | 3.19E–04 | |
| mRNA transcription | 41 | 19.32 | 6.14E–04 | |
| Cell adhesion | 18 | 5.71 | 6.99E–04 | |
| Ligand-mediated signaling | 14 | 3.35 | 1.82E–03 | |
| Cell cycle control | 14 | 3.61 | 3.05E–03 | |
| Skeletal development | 8 | 1.11 | 3.97E–03 | |
| Anterior/posterior patterning | 6 | 0.58 | 4.34E–03 | |
| Signal transduction | 60 | 37.94 | 5.43E–03 | |
| Oncogenesis | 13 | 3.97 | 6.84E–03 | |
| Ectoderm development | 18 | 6.19 | 9.23E–03 | |
| Muscle contraction | 8 | 1.73 | 1.27E–02 | |
| Cell proliferation and differentiation | 20 | 8.52 | 1.32E–02 | |
| Cell cycle | 20 | 8.53 | 1.34E–02 | |
| Neurogenesis | 16 | 5.4 | 2.61E–02 | |
| Apoptosis | 13 | 4.62 | 2.76E–02 | |
| Segment specification | 6 | 0.82 | 2.98E–02 |
| NS KD vs. Ctl ESCs | Biological Process | Count | Expected Count | P-value |
| Down-regulated | Glycolysis | 4 | 0.2 | 8.07E–03 |
| Chromosome segregation | 5 | 0.41 | 1.21E–02 | |
| Cell cycle | 11 | 3.49 | 2.40E–02 | |
| Developmental processes | 18 | 8.29 | 4.42E–02 | |
| Up-regulated | Developmental processes | 60 | 20.25 | 6.30E–13 |
| Cell structure and motility | 33 | 9.58 | 2.67E–08 | |
| Cell structure | 25 | 5.76 | 1.83E–07 | |
| Mesoderm development | 20 | 4.89 | 2.28E–05 | |
| mRNA transcription regulation | 36 | 14.32 | 7.97E–05 | |
| Cell communication | 29 | 10.67 | 1.94E–04 | |
| Embryogenesis | 10 | 1.42 | 3.19E–04 | |
| mRNA transcription | 41 | 19.32 | 6.14E–04 | |
| Cell adhesion | 18 | 5.71 | 6.99E–04 | |
| Ligand-mediated signaling | 14 | 3.35 | 1.82E–03 | |
| Cell cycle control | 14 | 3.61 | 3.05E–03 | |
| Skeletal development | 8 | 1.11 | 3.97E–03 | |
| Anterior/posterior patterning | 6 | 0.58 | 4.34E–03 | |
| Signal transduction | 60 | 37.94 | 5.43E–03 | |
| Oncogenesis | 13 | 3.97 | 6.84E–03 | |
| Ectoderm development | 18 | 6.19 | 9.23E–03 | |
| Muscle contraction | 8 | 1.73 | 1.27E–02 | |
| Cell proliferation and differentiation | 20 | 8.52 | 1.32E–02 | |
| Cell cycle | 20 | 8.53 | 1.34E–02 | |
| Neurogenesis | 16 | 5.4 | 2.61E–02 | |
| Apoptosis | 13 | 4.62 | 2.76E–02 | |
| Segment specification | 6 | 0.82 | 2.98E–02 |
Analysis was performed with the Panther classification system (http://www.pantherdb.org/tools/genexAnalysis.jsp). The biological process terms of the Panther classification system are similar to those of the Gene Ontology (GO), but abbreviated and simplified to facilitate high-throughput analyses. The set of all genes in the mouse genome was used as a reference list. Included in the table are the number of misregulated genes found in each category (count), the expected number of genes for each category among misregulated genes based on the reference list (expected count), and the P-value of enrichment as calculated by the binomial statistic, which is the probability that the number of genes observed in each category occurred by chance as determined by the reference list. Ns shRNA-1 was used for depletion of NS.