Skip to main content

Table 3 Gene Ontology (GO) terms enriched in significant proteins after repetitive somatic embryogenesis in Douglas-fir

From: Repetitive somatic embryogenesis induced cytological and proteomic changes in embryogenic lines of Pseudotsuga menziesii [Mirb.]

GO.ID Term Annot. Sign. Exp. ratio sign./exp. Expression
Secondary versus primary lines
 GO:0015977 carbon fixation 17 2 0.13 15.38 2ry > 1ry
 GO:0009269 response to desiccation 17 2 0.13 15.38 2ry > 1ry
 GO:0006099 tricarboxylic acid cycle 38 2 0.28 7.14 2ry > 1ry
 GO:0015979 photosynthesis 43 2 0.32 6.25 2ry > 1ry
 GO:0051603 proteolysis involved in cellular protein catabolic process 142 5 1.05 4.76 2ry > 1ry
 GO:0043488 regulation of mRNA stability 2 2 0.05 40.00 1ry > 2ry
 GO:0046292 formaldehyde metabolic process 4 2 0.1 20.00 1ry > 2ry
 GO:0006556 S-adenosylmethionine biosynthetic process 7 3 0.18 16.67 1ry > 2ry
 GO:0006097 glyoxylate cycle 7 3 0.18 16.67 1ry > 2ry
 GO:0010030 positive regulation of seed germination 5 2 0.13 15.38 1ry > 2ry
 GO:0051262 protein tetramerization 6 2 0.15 13.33 1ry > 2ry
 GO:1901663 quinone biosynthetic process 13 4 0.33 12.12 1ry > 2ry
 GO:0006558 L-phenylalanine metabolic process 15 4 0.38 10.53 1ry > 2ry
 GO:0009969 xyloglucan biosynthetic process 8 2 0.2 10.00 1ry > 2ry
 GO:0009051 pentose-phosphate shunt, oxidative branch 8 2 0.2 10.00 1ry > 2ry
 GO:0042593 glucose homeostasis 8 2 0.2 10.00 1ry > 2ry
 GO:0010262 somatic embryogenesis 14 3 0.35 8.57 1ry > 2ry
 GO:0006032 chitin catabolic process 22 4 0.55 7.27 1ry > 2ry
 GO:0009813 flavonoid biosynthetic process 58 9 1.46 6.16 1ry > 2ry
 GO:0002215 defense response to nematode 13 2 0.33 6.06 1ry > 2ry
 GO:0006730 one-carbon metabolic process 27 4 0.68 5.88 1ry > 2ry
 GO:0080167 response to karrikin 44 6 1.11 5.41 1ry > 2ry
 GO:0009699 phenylpropanoid biosynthetic process 93 12 2.34 5.13 1ry > 2ry
 GO:0008219 cell death 77 9 1.94 4.64 1ry > 2ry
 GO:0016998 cell wall macromolecule catabolic process 26 3 0.65 4.62 1ry > 2ry
 GO:0006555 methionine metabolic process 28 3 0.71 4.23 1ry > 2ry
 GO:0009611 response to wounding 129 13 3.25 4.00 1ry > 2ry
 GO:0009787 regulation of abscisic acid-activated signaling pathway 30 3 0.76 3.95 1ry > 2ry
 GO:0009411 response to UV 53 5 1.33 3.76 1ry > 2ry
 GO:0009808 lignin metabolic process 85 8 2.14 3.74 1ry > 2ry
 GO:0000272 polysaccharide catabolic process 64 6 1.61 3.73 1ry > 2ry
 GO:0009626 plant-type hypersensitive response 44 4 1.11 3.60 1ry > 2ry
 GO:0009636 response to toxic substance 49 4 1.23 3.25 1ry > 2ry
 GO:0031408 oxylipin biosynthetic process 51 4 1.28 3.13 1ry > 2ry
 GO:0055114 oxidation-reduction process 684 36 17.22 2.09 1ry > 2ry
Tertiary versus secondary lines
 GO:0006433 prolyl-tRNA aminoacylation 2 2 0.06 33.33 3ry > 2ry
 GO:0009871 jasmonic acid and ethylene-dependent systemic resistance. Ethylene mediated signaling pathway 5 3 0.16 18.75 3ry > 2ry
 GO:0009969 xyloglucan biosynthetic process 8 3 0.26 11.54 3ry > 2ry
 GO:0031640 killing of cells of other organism 11 4 0.35 11.43 3ry > 2ry
 GO:0010731 protein glutathionylation 7 2 0.22 9.09 3ry > 2ry
 GO:0010183 pollen tube guidance 14 4 0.45 8.89 3ry > 2ry
 GO:0006558 L-phenylalanine metabolic process 15 4 0.48 8.33 3ry > 2ry
 GO:0046487 glyoxylate metabolic process 8 2 0.26 7.69 3ry > 2ry
 GO:0080092 regulation of pollen tube growth 17 4 0.54 7.41 3ry > 2ry
 GO:0043650 dicarboxylic acid biosynthetic process 13 3 0.41 7.32 3ry > 2ry
 GO:0006032 chitin catabolic process 22 5 0.7 7.14 3ry > 2ry
 GO:0046189 phenol-containing compound biosynthetic process 9 2 0.29 6.90 3ry > 2ry
 GO:0006949 syncytium formation 9 2 0.29 6.90 3ry > 2ry
 GO:0080167 response to karrikin 44 8 1.4 5.71 3ry > 2ry
 GO:0006816 calcium ion transport 11 2 0.35 5.71 3ry > 2ry
 GO:0009828 plant-type cell wall loosening 11 2 0.35 5.71 3ry > 2ry
 GO:0009626 plant-type hypersensitive response 44 7 1.4 5.00 3ry > 2ry
 GO:0000272 polysaccharide catabolic process 64 10 2.04 4.90 3ry > 2ry
 GO:0072329 monocarboxylic acid catabolic process 42 6 1.34 4.48 3ry > 2ry
 GO:0006749 glutathione metabolic process 56 8 1.79 4.47 3ry > 2ry
 GO:0031408 oxylipin biosynthetic process 51 7 1.63 4.29 3ry > 2ry
 GO:0009718 anthocyanin-containing compound biosynthetic process 23 3 0.73 4.11 3ry > 2ry
 GO:0019395 fatty acid oxidation 39 5 1.24 4.03 3ry > 2ry
 GO:0009611 response to wounding 129 15 4.11 3.65 3ry > 2ry
 GO:0050832 defense response to fungus 102 11 3.25 3.38 3ry > 2ry
 GO:0009699 phenylpropanoid biosynthetic process 93 10 2.96 3.38 3ry > 2ry
 GO:0009808 lignin metabolic process 85 9 2.71 3.32 3ry > 2ry
 GO:0006952 defense response 370 31 11.79 2.63 3ry > 2ry
 GO:0044248 cellular catabolic process 472 39 15.05 2.59 3ry > 2ry
 GO:0006979 response to oxidative stress 232 16 7.4 2.16 3ry > 2ry
 GO:0009617 response to bacterium 201 13 6.41 2.03 3ry > 2ry
 GO:0055114 oxidation-reduction process 684 44 21.8 2.02 3ry > 2ry
 GO:0051603 proteolysis involved in cellular protein catabolic process 142 9 4.53 1.99 3ry > 2ry
 GO:0005975 carbohydrate metabolic process 414 24 13.2 1.82 3ry > 2ry
 GO:0010038 response to metal ion 393 19 12.53 1.52 3ry > 2ry
 GO:0006879 cellular iron ion homeostasis 3 2 0.03 66.67 2ry > 3ry
 GO:0010197 polar nucleus fusion 8 2 0.09 22.22 2ry > 3ry
 GO:0046274 lignin catabolic process 16 2 0.18 11.11 2ry > 3ry
 GO:0048509 regulation of meristem development 20 2 0.23 8.70 2ry > 3ry
 GO:0010051 xylem and phloem pattern formation 24 2 0.27 7.41 2ry > 3ry
 GO:0000398 mRNA splicing. Via spliceosome 56 4 0.63 6.35 2ry > 3ry
 GO:0016310 phosphorylation 222 6 2.51 2.39 2ry > 3ry
 GO:0032774 RNA biosynthetic process 262 7 2.97 2.36 2ry > 3ry
  1. GO.ID: Gene Ontology Identifiant; Annot.: number of annotated Douglas proteins with GO terms in the data set; Sign.: number of Douglas proteins in the analysed dataset; Exp.: expected number of interesting proteins mapped to the GO term if randomly distributed over all GO terms; ratio sign./exp: ratio between significant and expected proteins mapping to the GO term; Expression: proteins assigned to specific GO term are over-expressed in 1ry (1ry > 2ry), 2ry (2ry > 1ry) or 3ry lines (3ry > 2ry). Only results with pvalue < 0.05 of the Fisher’s exact test were considered