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Table 3 Overrepresented Gene Ontology biological process terms in Gb or Gh fiber. Transcripts that had higher expression (fold change ≥2) on at least one DPA in the cross genotype comparison were analyzed for over-representation of GO biological process terms (p < 0.006, q < 0.05). FDR q-values were determined as in Table 1 (see p-values in Additional file 14)

From: Metabolomic and transcriptomic insights into how cotton fiber transitions to secondary wall synthesis, represses lignification, and prolongs elongation

Up in Gb fiber Up in Gh fiber
GO:0042254 ribosome biogenesis 1.15E-09 GO:0015996 chlorophyll catabolic process 3.92E-06
GO:0042026 protein refolding 3.28E-05 GO:0010150 leaf senescence 3.92E-06
GO:0010143 cutin biosynthetic process 2.11E-04 GO:0019745 pentacyclic triterpenoid biosynthetic process 3.92E-06
GO:0006730 one-carbon metabolic process 2.01E-03 GO:0006090 pyruvate metabolic process 1.02E-05
GO:0006821 chloride transport 2.81E-03 GO:0009414 response to water deprivation 2.89E-05
GO:0006448 regulation of translational elongation 9.92E-03 GO:0006013 mannose metabolic process 1.23E-04
GO:0006536 glutamate metabolic process 1.00E-02 GO:0006094 gluconeogenesis 1.78E-04
GO:0009637 response to blue light 1.60E-02 GO:0006096 glycolysis 2.07E-04
GO:0015808 L-alanine transport 1.63E-02 GO:0006000 fructose metabolic process 3.34E-04
GO:0050732 negative regulation of peptidyl-tyrosine phosphorylation 1.63E-02 GO:0009651 response to salt stress 4.62E-04
GO:0051085 chaperone mediated protein folding requiring cofactor 1.63E-02 GO:0010193 response to ozone 1.11E-03
GO:0048640 negative regulation of developmental growth 1.63E-02 GO:0016556 mRNA modification 1.27E-03
GO:0072521 purine-containing compound metabolic process 2.76E-02 GO:0009965 leaf morphogenesis 1.34E-03
GO:0006639 acylglycerol metabolic process 2.76E-02 GO:0010363 regulation of plant-type hypersensitive response 1.97E-03
GO:0051302 regulation of cell division 2.76E-02 GO:0052542 defense response by callose deposition 2.47E-03
GO:0006909 phagocytosis 2.76E-02 GO:0030048 actin filament-based movement 2.47E-03
GO:0046653 tetrahydrofolate metabolic process 2.76E-02 GO:0009834 secondary cell wall biogenesis 2.47E-03
GO:0006123 mitochondrial electron transport, cytochrome c to oxygen 2.76E-02 GO:0019643 reductive tricarboxylic acid cycle 3.29E-03
GO:0006497 protein lipidation 4.45E-02 GO:0010167 response to nitrate 4.00E-03
GO:0009220 pyrimidine ribonucleotide biosynthetic process 4.50E-02 GO:0000165 MAPK cascade 5.62E-03
GO:0015865 purine nucleotide transport 4.50E-02 GO:0045492 xylan biosynthetic process 6.01E-03
GO:0015721 bile acid and bile salt transport 4.50E-02 GO:0010413 glucuronoxylan metabolic process 6.01E-03
GO:0015701 bicarbonate transport 4.50E-02 GO:0050832 defense response to fungus 6.46E-03
GO:0009116 nucleoside metabolic process 4.59E-02 GO:0051567 histone H3-K9 methylation 6.99E-03
GO:0008033 tRNA processing 4.74E-02 GO:0071805 potassium ion transmembrane transport 6.99E-03
    GO:0043068 positive regulation of programmed cell death 6.99E-03
    GO:0010200 response to chitin 8.09E-03
    GO:0000910 cytokinesis 9.02E-03
    GO:0019344 cysteine biosynthetic process 9.46E-03
    GO:0007030 Golgi organization 1.03E-02