Skip to main content

Table 2 Catalog of specific biological processes statistically over-represented during fiber developmental stages of TM-1 and im mutant (FDR < 0.05)

From: Aberrant phenotype and transcriptome expression during fiber cell wall thickening caused by the mutation of the Im gene in immature fiber (im) mutant in Gossypium hirsutum L

Developmental stage comparison Process upregulated in TM-1 or im GO annotation Functional categories FDR
16 vs. 13 DPA, up-regulated at 16 DPA TM-1 GO:0009834 Secondary cell wall biogenesis 1.7E-04
   GO:0010417 Glucuronoxylan biosynthetic process 2.7E-04
  im NA NA NA
16 vs. 13 dpa, up-regulated at 13 DPA TM-1 GO:0009813 Flavonoid biosynthetic process 7.1E-10
   GO:0010466 Negative regulation of peptidase activity 3.1E-02
  im GO:0043617 Cellular response to sucrose starvation 8.9E-04
   GO:0006529 Asparagine biosynthetic process 9.3E-04
   GO:0009744 Response to sucrose stimulus 9.8E-03
   GO:0009646 Response to absence of light 9.8E-03
   GO:0009063 Cellular amino acid catabolic process 1.2E-02
   GO:0009750 Response to fructose stimulus 1.7E-02
   GO:0006541 Glutamine metabolic process 2.2E-02
   GO:0009749 Response to glucose stimulus 3.1E-02
   GO:0009835 Ripening 3.3E-02
19 vs. 16 DPA, up-regulated at 19 DPA TM-1 NA NA NA
  im GO:0009834 Secondary cell wall biogenesis 1.3E-03
   GO:0030244 Cellulose biosynthetic process 6.0E-03
   GO:0007047 Cellular cell wall organization 7.9E-03
   GO:0010417 Glucuronoxylan biosynthetic process 4.1E-02
19 vs. 16 DPA, up-regulated at 16 DPA TM-1 GO:0010025 Wax biosynthetic process 7.7E-05
   GO:0009664 Plant-type cell wall organization 1.6E-02
   GO:0006723 Cuticle hydrocarbon biosynthetic process 1.6E-02
   GO:0009826 Unidimensional cell growth 3.1E-02
  im GO:0043086 Negative regulation of catalytic activity 2.2E-02
22 vs. 19 DPA, up-regulated at 22 DPA TM-1 GO:0010200 Response to chitin 2.0E-05
   GO:0050832 Defense response to fungus 6.1E-03
   GO:0009738 Abscisic acid mediated signaling pathway 2.8E-02
  im GO:0010200 Response to chitin 9.0E-04
   GO:0050832 Defense response to fungus 2.9E-02
   GO:0001666 Response to hypoxia 3.7E-02
22 vs. 19 DPA, up-regulated at 19 DPA TM-1 GO:0009834 Secondary cell wall biogenesis 2.2E-03
   GO:0016126 Sterol biosynthetic process 1.8E-02
   GO:0035435 Phosphate transmembrane transport 2.6E-02
  im GO:0010025 Wax biosynthetic process 1.9E-08
   GO:0000038 Very-long-chain fatty acid metabolic process 1.3E-04
   GO:0035435 Phosphate transmembrane transport 1.0E-02
   GO:0006723 Cuticle hydrocarbon biosynthetic process 4.3E-02
25 vs. 22 DPA, up-regulated at 25 DPA TM-1 GO:0043617 Cellular response to sucrose starvation 1.5E-02
   GO:0006529 Asparagine biosynthetic process 1.5E-02
  im NA NA NA
25 vs. 22 DPA, up-regulated at 22 dpa TM-1 GO:0009809 Lignin biosynthetic process 1.8E-03
  im GO:0010200 Response to chitin 8.0E-17
   GO:0010120 Camalexin biosynthetic process 2.3E-02
   GO:0050832 Defense response to fungus 4.0E-02
   GO:0000169 Activation of MAPK activity involved in osmosensory signaling pathway 4.9E-02
  1. NA, no result.
  2. FDR, false discovery rate.