Table 3.
GSEA of Biological pathways in groups defined by “case-control” contrasts.
| Significant enrichment scores based on GSEA | ||
|---|---|---|
| 2008 | 2013 | |
| Nervous System processes | ||
| Nervous system development | −0.3724 | 0.3875 |
| Central nervous system development | −0.4466 | 0.4619 |
| Generation of neurons | −0.4522 | 0.3904 |
| Neuron differentiation | −0.4678 | 0.4064 |
| Neurogenesis | −0.4704 | 0.426 |
| Brain development | −0.5241 | NS |
| Neurite development | NS | 0.4524 |
| Neuron development | NS | 0.4475 |
| Regulation processes | ||
| Negative regulation of nucleobase nucleoside nucleotide and nucleic acid metabolic process | −0.3366 | NS |
| Negative regulation of cellular metabolic process | −0.3661 | NS |
| Positive regulation of nucleobase nucleoside nucleotide and nucleic acid metabolic process | −0.5359 | NS |
| Positive regulation of transcription DNA dependent | −0.5537 | NS |
| Positive regulation of RNA metabolic process | −0.5589 | NS |
| Negative regulation of transcription DNA dependent | −0.3836 | NS |
| Negative regulation of cellular process | −0.3618 | NS |
| Regulation of developmental process | −0.3511 | NS |
| Regulation of transcription from RNA polymerase II promoter | −0.3982 | NS |
| Regulation of cellular metabolic process | −0.36 | NS |
| Regulation of gene expression. | −0.3292 | NS |
| Positive regulation of developmental process | −0.3546 | NS |
| Positive regulation of metabolic process | −0.5421 | NS |
| Regulation of transcription DNA dependent | −0.4831 | NS |
| Negative regulation of transcription | −0.3385 | NS |
| Negative regulation of RNA metabolic process | −0.3754 | NS |
| Positive regulation of cellular metabolic process | −0.4082 | NS |
| Positive regulation of biological process | −0.4049 | NS |
| Negative regulation of metabolic process | −0.3613 | NS |
| Regulation of metabolic process | −0.3607 | NS |
| Regulation of RNA metabolic process | −0.3869 | NS |
| Positive regulation of cellular process | −0.4088 | NS |
| Regulation of nucleobase nucleoside nucleotide and nucleic acid metabolic process | −0.3319 | 0.3038 |
| Negative regulation of biological process | −0.3715 | NS |
| Regulation of transcription | −0.3252 | 0.3122 |
| Positive regulation of transcription | −0.5666 | NS |
| Development processes | NS | |
| System development | −0.3819 | 0.3671 |
| Cell development | −0.3795 | NS |
| Multicellular organismal development | −0.3767 | 0.368 |
| Anatomical structure development | −0.3944 | 0.3279 |
| Organ development | −0.42 | 0.4024 |
| Tissue development | NS | 0.4646 |
| Processes involved with protein and protein synthesis | ||
| RNA metabolic process | −0.373 | NS |
| Nucleobase nucleoside nucleotide and nucleic acid metabolic process | −0.3783 | NS |
| Transcription DNA dependente | −0.3912 | 0.3193 |
| RNA biosynthetic process | −0.3928 | NS |
| Post translational protein modification | −0.417 | NS |
| Transcription | −0.391 | 0.3193 |
| Protein modification process | −0.4134 | NS |
| Protein aminoacid phosphorylation | −0.3827 | NS |
| Transcription from RNA polymerase II promoter | −0.4092 | NS |
| Protein amino acid dephosphorylation | −0.4928 | NS |
| Protein metabolic process | NS | 0.3637 |
| Other processes | ||
| Cell migration | NS | 0.4125 |
| Signal transduction | −0.3471 | 0.317 |
| Cell surface receptor linked signal transduction GO: 0007166 | NS | 0.2819 |
| Anatomical structure morphogenesis | −0.3608 | 0.2994 |
| Locomotory behavior | −0.1731 | NS |
| Biopolymer metabolic process | −0.3539 | NS |
| Biopolymer modification | −0.4122 | NS |
| Dephosphorylation | −0.5187 | NS |
| Phosphorylation | −0.3469 | NS |
Note: GSEA, Gene set enrichment analysis; NS, No significant (p > 0.001). All biological pathways significant at false discovery rate (FDR) correction. Signal negative represents DNA hypomethylated biological pathways.