Table 2.
Gene Ontology Biological Process Terms Enriched in genes differentially expressed by Age. 1574 genes were differentially expressed by age (Fig 3; p.adj < 0.01; fold change > 2) relative to prominence and layer-matched samples. 342 differed at E10.5, 598 differed at E11.5 & 1122 differed at E12.5. The top-ranked GO Biological Process terms for E10.5, E11.5 and E12.5 are respectively highlighted with light green, teal and dark green. Analysis and abbreviations are described in Table 1.
Age+dependent gene functions based on enrichment in Gene Ontology Biological Process terms
| GO Biological Process Term | Pop.Hits | E 10.5 | E 11.5 | E 12.5 | best age | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
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| |||||||||||
| Count | Fold.Enrich | p.adj | Count | Fold.Enrich | p.adj | Count | Fold.Enrich | p.adj | |||
| GO:0001763~morphogenesis of a branching structure | 125 | 14 | 6.56 | 1.62EI04 | 17 | 4.22 | 6.11EI05 | 24 | 3.19 | 5.88EI05 | all |
|
| |||||||||||
| GO:0009069~serine family amino acid metabolic process | 22 | 5 | 13.31 | 2.56EI02 | NA | NA | NA | NA | NA | NA | 10.5 |
| GO:0044271~nitrogen compound biosynthetic process | 302 | 15 | 2.91 | 3.11EI02 | NA | NA | NA | NA | NA | NA | 10.5 |
| GO:0006544~glycine metabolic process | 12 | 4 | 19.52 | 4.17EI02 | NA | NA | NA | NA | NA | NA | 10.5 |
|
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| GO:0045165~cell fate commitment | 147 | 15 | 5.98 | 1.10EI04 | 25 | 5.28 | 1.07EI08 | 17 | 1.92 | 1.77EI01 | 10.5, 11.5 |
| GO:0048010~vascular endothelial growth factor receptor signaling pathway | 14 | 3 | 12.55 | 2.71EI01 | 5 | 11.08 | 1.18EI02 | NA | NA | NA | 10.5, 11.5 |
|
| |||||||||||
| GO:0007423~sensory organ development | 257 | 13 | 2.96 | 5.75EI02 | 37 | 4.47 | 7.84EI11 | 29 | 1.87 | 3.09EI02 | 11.5 |
| GO:0001656~metanephros development | 58 | 7 | 7.07 | 2.49EI02 | 16 | 8.56 | 3.01EI08 | 15 | 4.29 | 2.26EI04 | 11.5 |
| GO:0035107~appendage morphogenesis | 115 | 11 | 5.60 | 5.22EI03 | 21 | 5.67 | 6.37EI08 | 17 | 2.45 | 2.64EI02 | 11.5 |
| GO:0045664~regulation of neuron differentiation | 102 | 5 | 2.87 | 5.80EI01 | 18 | 5.47 | 1.05EI06 | 12 | 1.95 | 3.55EI01 | 11.5 |
| GO:0050678~regulation of epithelial cell proliferation | 63 | 4 | 3.72 | 5.69EI01 | 13 | 6.40 | 1.78EI05 | 12 | 3.16 | 2.34EI02 | 11.5 |
| GO:0014033~neural crest cell differentiation | 33 | 4 | 7.10 | 2.30EI01 | 10 | 9.40 | 1.82EI05 | 7 | 3.52 | 1.53EI01 | 11.5 |
| GO:0021537~telencephalon development | 72 | NA | NA | NA | 12 | 5.17 | 3.45EI04 | 11 | 2.53 | 1.31EI01 | 11.5 |
| GO:0001756~somitogenesis | 41 | NA | NA | NA | 9 | 6.81 | 7.52EI04 | 9 | 3.64 | 4.53EI02 | 11.5 |
| GO:0042573~retinoic acid metabolic process | 17 | NA | NA | NA | 6 | 10.95 | 2.53EI03 | 4 | 3.90 | 5.00EI01 | 11.5 |
| GO:0030111~regulation of Wnt receptor signaling pathway | 39 | NA | NA | NA | 8 | 6.36 | 3.52EI03 | 9 | 3.83 | 3.44EI02 | 11.5 |
| GO:0021983~pituitary gland development | 29 | NA | NA | NA | 7 | 7.49 | 4.39EI03 | 5 | 2.86 | 5.48EI01 | 11.5 |
| GO:0045445~myoblast differentiation | 12 | 3 | 14.64 | 2.20EI01 | 5 | 12.93 | 6.67EI03 | NA | NA | NA | 11.5 |
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| GO:0016337~cell-cell adhesion | 236 | NA | NA | NA | 32 | 4.21 | 8.19EI09 | 48 | 3.37 | 9.61EI11 | 11.5, 12.5 |
| GO:0007409~axonogenesis | 163 | 10 | 3.59 | 6.40EI02 | 26 | 4.95 | 1.28EI08 | 38 | 3.87 | 3.22EI10 | 11.5, 12.5 |
| GO:0045944~positive regulation of transcription from RNA polymerase II promoter | 358 | 15 | 2.45 | 8.89EI02 | 37 | 3.21 | 9.45EI08 | 53 | 2.46 | 2.76EI07 | 11.5, 12.5 |
| GO:0030198~extracellular matrix organization | 101 | 6 | 3.48 | 3.15EI01 | 15 | 4.61 | 9.38EI05 | 26 | 4.27 | 1.04EI07 | 11.5, 12.5 |
| GO:0007169~transmembrane receptor protein tyrosine kinase signaling pathway | 192 | 8 | 2.44 | 4.04EI01 | 23 | 3.72 | 8.06EI06 | 32 | 2.77 | 2.01EI05 | 11.5, 12.5 |
| GO:0007267~cell-cell signaling | 290 | 12 | 2.42 | 1.69EI01 | 26 | 2.78 | 1.59EI04 | 43 | 2.46 | 5.21EI06 | 11.5, 12.5 |
| GO:0048514~blood vessel morphogenesis | 198 | 11 | 3.25 | 6.89EI02 | 21 | 3.29 | 1.31EI04 | 29 | 2.43 | 7.07EI04 | 11.5, 12.5 |
| GO:0014706~striated muscle tissue development | 127 | NA | NA | NA | 16 | 3.91 | 2.87EI04 | 24 | 3.14 | 7.58EI05 | 11.5, 12.5 |
| GO:0022612~gland morphogenesis | 84 | 8 | 5.58 | 2.86EI02 | 13 | 4.80 | 3.00EI04 | 20 | 3.95 | 1.98EI05 | 11.5, 12.5 |
| GO:0048565~gut development | 39 | 4 | 6.01 | 3.11EI01 | 8 | 6.36 | 3.52EI03 | 10 | 4.25 | 9.80EI03 | 11.5, 12.5 |
| GO:0016055~Wnt receptor signaling pathway | 130 | NA | NA | NA | 14 | 3.34 | 4.51EI03 | 22 | 2.81 | 9.97EI04 | 11.5, 12.5 |
| GO:0030509~BMP signaling pathway | 24 | 3 | 7.32 | 4.70EI01 | 6 | 7.76 | 1.22EI02 | 7 | 4.84 | 4.22EI02 | 11.5, 12.5 |
| GO:0060324~face development | 17 | NA | NA | NA | 5 | 9.12 | 2.34EI02 | 7 | 6.83 | 8.10EI03 | 11.5, 12.5 |
| GO:0042476~odontogenesis | 45 | 4 | 5.21 | 3.76EI01 | 7 | 4.83 | 3.79EI02 | 12 | 4.42 | 1.68EI03 | 11.5, 12.5 |
| GO:0051145~smooth muscle cell differentiation | 10 | NA | NA | NA | 4 | 12.41 | 4.13EI02 | 5 | 8.30 | 3.56EI02 | 11.5, 12.5 |
|
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| GO:0060348~bone development | 118 | 6 | 2.98 | 4.21EI01 | 16 | 4.21 | 1.22EI04 | 29 | 4.08 | 3.22EI08 | 12.5 |
| GO:0051216~cartilage development | 78 | NA | NA | NA | 13 | 5.17 | 1.43EI04 | 22 | 4.68 | 3.81EI07 | 12.5 |
| GO:0042692~muscle cell differentiation | 117 | NA | NA | NA | 15 | 3.98 | 4.50EI04 | 25 | 3.55 | 5.14EI06 | 12.5 |
| GO:0008544~epidermis development | 125 | NA | NA | NA | 10 | 2.48 | 1.68EI01 | 24 | 3.19 | 5.88EI05 | 12.5 |
| GO:0007178~transmembrane receptor protein serine/threonine kinase signaling pathway | 78 | 5 | 3.75 | 3.94EI01 | 10 | 3.98 | 1.22EI02 | 18 | 3.83 | 1.15EI04 | 12.5 |
| GO:0048634~regulation of muscle development | 43 | NA | NA | NA | NA | NA | NA | 13 | 5.02 | 2.15EI04 | 12.5 |
| GO:0048638~regulation of developmental growth | 37 | NA | NA | NA | 5 | 4.19 | 2.32EI01 | 12 | 5.38 | 2.54EI04 | 12.5 |
| GO:0051797~regulation of hair follicle development | 7 | NA | NA | NA | 3 | 13.30 | 1.69EI01 | 5 | 11.85 | 9.61EI03 | 12.5 |
| GO:0008593~regulation of Notch signaling pathway | 8 | NA | NA | NA | 3 | 11.63 | 2.05EI01 | 5 | 10.37 | 1.57EI02 | 12.5 |