Table 3.
Ontology analysis of molecular and cellular components up-regulated at 3 days compared with 0 days.
| Annotation | Gene Set | z-score * |
|---|---|---|
| Angiogenesis mediated signaling pathway | ||
| Regulation of BMP signaling pathway | 26 | 5.97 |
| Transmembrane receptor protein serine/threonine kinase signaling pathway | 139 | 4.95 |
| BMP signaling pathway | 60 | 3.8 |
| Regulation of transforming growth factor beta receptor signaling pathway | 68 | 3.54 |
| Transforming growth factor beta receptor signaling pathway | 114 | 2.6 |
| Cytokine related | ||
| Cytokine biosynthetic process | 83 | 3.15 |
| Cytokine metabolic process | 84 | 3.13 |
| Enzyme linked receptor protein signaling pathway | 416 | 2.45 |
| Cell response to stress | ||
| Nucleus organization | 48 | 4.3 |
| Positive regulation of cellular process | 1664 | 3.51 |
| Positive regulation of biological process | 1832 | 3.24 |
| Positive regulation of cell communication | 298 | 3.1 |
| Intracellular signaling cascade | 1501 | 2.96 |
| Cellular component disassembly | 116 | 2.57 |
| Cell communication | 3954 | 2.33 |
| Cellular response to stimulus | 979 | 2.07 |
| Defense response | 628 | 1.73 |
| Inflammatory reactions | ||
| Inflammatory response | 349 | 2.78 |
| Regulation of immune system process | 357 | 2.74 |
| Viral reproduction | 82 | 3.17 |
| Regulation of immune system process | 357 | 2.74 |
| Leukocyte mediated immunity | 126 | 2.44 |
| Immune system process | 1013 | 2 |
| Cell differentiation | ||
| Erythrocyte differentiation | 57 | 3.91 |
| Osteoblast differentiation | 3.6 | 3.58 |
| Positive regulation of developmental process | 641 | 2.96 |
| Gonad development | 103 | 2.77 |
| Myeloid cell differentiation | 140 | 2.27 |
| Muscle tissue development | 168 | 2.01 |
| Cell or tissue repair | ||
| DNA repair | 278 | 3.25 |
| Cellular response to DNA damage stimulus | 325 | 2.93 |
| Response to DNA damage stimulus | 359 | 2.73 |
| Homeostasis of number of cells | 112 | 2.63 |
| Multicellular organism reproduction | 121 | 2.5 |
| Reproductive process in a multicellular organism | 121 | 2.5 |
| Positive regulation of apoptosis | 416 | 2.45 |
| Positive regulation of programmed cell death | 419 | 2.44 |
| Positive regulation of cell death | 421 | 2.43 |
| Cellular protein metabolic process | 2492 | 2.39 |
| Positive regulation of protein kinase cascade | 160 | 2.08 |
| Cellular biopolymer metabolic process | 5649 | 1.74 |
| Cellular macromolecule metabolic process | 5763 | 1.68 |
| Cellular biopolymer catabolic process | 691 | 1.58 |
| Biopolymer metabolic process | 6067 | 15 |
*
z-score, calculated in GeneScifter, detailed formula is presented in Supplemental Method.