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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 ID GO Name FDR GO ID GO Name FDR
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