Table 2. Top 20 and phenotype reflecting enriched biological processes.
The enriched biological processes, ranked based on NES and FDR value, are shown. The enriched biological processes, detected by the GSEA analysis, were statistically significant (no asterisk: FDR < 0.0001, *: FDR < 0.05 and **: FDR < 0.01). The phenotype reflecting enriched biological processes are shown under dashed-line ‡: Full name is provided in Data S2.
| Ag | SiO2 | |||||||
|---|---|---|---|---|---|---|---|---|
| Biological process | NES | Rank | NES | Rank | ||||
| Positive enrichment | ||||||||
| Cellular process | Cell cycle | 6.591 | 2 | Cell cycle | 4.095 | 2 | ||
| Cell cycle process | 6.624 | 1 | Cell cycle process | 4.167 | 1 | |||
| Meiotic cell cycle | 5.455 | 10 | Meiotic cell cycle | 3.413 | 10 | |||
| Meiotic cell cycle process | 4.744 | 15 | _ | _ | _ | |||
| Meiotic nuclear division | 5.215 | 12 | Meiotic nuclear division | 3.158 | 12 | |||
| Meiotic chromosome segregation | 4.441 | 18 | _ | _ | _ | |||
| Mitotic cell cycle | 4.805 | 14 | Mitotic cell cycle | 2.776 | 19 | |||
| Regulation of cell cycle | 4.378 | 20 | _ | _ | _ | |||
| Cell division | 4.561 | 17 | Cell division | 2.886 | 14 | |||
| Death&cell death | 6.022 | 4 | Death&cell death | 3.699 | 7 | |||
| Programmed cell death | 5.736 | 7 | Programmed cell death | 3.695 | 8 | |||
| Apoptotic process | 6.332 | 3 | Apoptotic process | 3.887 | 5 | |||
| Chromosome segregation | 4.943 | 13 | _ | _ | _ | |||
| Posttranscriptional gene silencing&gene silencing | 4.407 | 19 | _ | _ | _ | |||
| Growth | _ | _ | _ | Developmental growth | 2.771 | 20 | ||
| _ | _ | _ | Regulation of growth | 2.787 | 18 | |||
| Metabolic process | Posttranscriptional regulation of gene gene expression | 4.571 | 16 | _ | _ | _ | ||
| Multicellular organism process | _ | _ | _ | Positive regulation of multicellular organismal process | 2.814 | 16 | ||
| Multi-organism process | Sexual reproduction | 5.713 | 8 | Sexual reproduction | 3.854 | 6 | ||
| Gamete generation | 5.982 | 5 | Gamete generation | 4.012 | 3 | |||
| Germ cell development&cellular process † | 5.334 | 11 | Germ cell development& cellular process † | 3.897 | 4 | |||
| _ | _ | _ | Female gamete generation | 2.813 | 17 | |||
| _ | _ | _ | Oogenesis | 3.010 | 13 | |||
| _ | _ | _ | Spermatid differentiation& spermatid development | 2.818 | 15 | |||
| Cellular component organization or biogenesis | Organelle fission | 5.756 | 6 | Organelle fission | 3.433 | 9 | ||
| Nuclear division | 5.621 | 9 | Nuclear division | 3.364 | 11 | |||
| Negative enrichment | ||||||||
| Behavior | Single organism behavior | −4.631 | 1 | _ | _ | _ | ||
| Cellular process | Cell communication | −4.285 | 7 | Aromatic compound biosynthetic process | −5.477 | 11 | ||
| Cell surface receptor signaling pathway | −4.082 | 17 | Regulation of cellular metabolic process | −5.198 | 19 | |||
| Developmental process | Cell morphogenesis | −4.571 | 3 | _ | _ | _ | ||
| Cell projection morphogenesis | −4.576 | 2 | _ | _ | _ | |||
| Cell part morphogenesis | −4.276 | 8 | _ | _ | _ | |||
| Generation of neurons | −4.048 | 20 | _ | _ | _ | |||
| Metabolic process | ||||||||
| _ | _ | _ | Cellular nitrogen compound biosynthetic process | −5.306 | 16 | |||
| _ | _ | _ | Heterocycle biosynthetic process | −5.423 | 12 | |||
| _ | _ | _ | Nucleobase containing compound biosynthetic process | −5.486 | 10 | |||
| _ | _ | _ | Organic cyclic compound biosynthetic process | −5.323 | 15 | |||
| _ | _ | _ | Positive regulation of gene expression | −5.029 | 20 | |||
| _ | _ | _ | Regulation of biosynthetic process& † | −5.410 | 13 | |||
| _ | _ | _ | Regulation of macromolecule biosynthetic process | −5.267 | 17 | |||
| _ | _ | _ | Regulation of cellular macromolecule biosynthetic process | −5.260 | 18 | |||
| _ | _ | _ | Regulation of nitrogen compound metabolic process& † | −5.587 | 9 | |||
| _ | _ | _ | Regulation of primary metabolic process | −5.406 | 14 | |||
| Regulation of rna metabolic process | −4.138 | 15 | Regulation of rna metabolic process | −5.971 | 2 | |||
| Rna biosynthetic process | −4.198 | 12 | Rna biosynthetic process | −5.923 | 3 | |||
| Nucleic acid templated transcription | −4.121 | 16 | Nucleic acid templated transcription | −5.833 | 6 | |||
| Regulation of rna biosynthetic process | −4.164 | 14 | Regulation of rna biosynthetic process | −5.983 | 1 | |||
| Transcription dna templated | −4.200 | 11 | Transcription dna templated | −5.864 | 5 | |||
| Regulation of transcription dna templated& † | −4.062 | 19 | Regulation of transcription dna templated& † | −5.805 | 7 | |||
| Transcription from rna polymerase ii promoter | −4.268 | 9 | Transcription from rna polymerase ii promoter | −5.881 | 4 | |||
| Regulation of transcription from rna poly. † | −4.192 | 13 | Regulation of transcription from rna poly. † | −5.775 | 8 | |||
| Multicellular organism development | Nervous system development | −4.528 | 4 | _ | _ | _ | ||
| Response to stimulus | Response to external stimulus | −4.493 | 5 | _ | _ | _ | ||
| Taxis | −4.066 | 18 | _ | _ | _ | |||
| Signaling | Signaling | −4.266 | 10 | _ | _ | _ | ||
| Single organism signaling | −4.299 | 6 | _ | _ | _ | |||
| Phenotype reflecting | ||||||||
| Growth | Regulation of cell growth** | −2.326 | 167 | Regulation of cell growth* | −1.714 | 410 | ||
| Locomotion | Regulation of locomotion | −3.124 | 66 | Regulation of locomotion | −3.694 | 86 | ||
| Reproduction | Regulation of reproductive process** | −2.476 | 132 | Regulation of reproductive process** | −2.062 | 294 | ||