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Table 3 The first ten ranked GO terms represented within the QTLs controlling number of sylleptic branches

From: Integrating genome annotation and QTL position to identify candidate genes for productivity, architecture and water-use efficiency in Populus spp

  GO ID Name P-valuea Countb Ontologyc
Model-based gene set analysis
GO:0015802 Basic amino acid transport 0.9050 9 / 26 P
GO:0009741 Response to brassinosteroid stimulus 0.8964 22 / 124 P
GO:0010440 Stomatal lineage progression 0.8092 5 / 10 P
GO:0004181 Metallocarboxypeptidase activity 0.6898 3 / 4 F
GO:0000170 Sphingosine hydroxylase activity 0.6842 3 / 3 F
GO:0048830 Adventitious root development 0.61586 8 / 13 P
GO:0000220 Vacuolar proton-transporting V-type ATPase. V0 domain 0.5584 3 / 4 C
GO:0006122 Mitochondrial electron transport. ubiquinol to cytochrome c 0.5481 4 / 8 P
GO:0045309 Protein phosphorylated amino acid binding 0.5478 6 / 13 F
GO:0010222 Stem vascular tissue pattern formation 0.5430 3 / 5 P
Topology-Weighted
GO:0048830 Adventitious root development 1.8770 e-07 8 / 13 P
GO:0009641 Shade avoidance 3.4385 e-07 9 / 18 P
GO:0003700 Sequence-specific DNA binding transcription factor activity 6.7533 e-07 210 / 2475 M
GO:0001071 Nucleic acid binding transcription factor activity 6.7533 e-07 210 / 2475 M
GO:0000976 Transcription regulatory region sequence-specific DNA binding 6.7533 e-07 210 / 2475 M
GO:0044212 Transcription regulatory region DNA binding 6.7533 e-07 210 / 2475 M
GO:0000975 Regulatory region DNA binding 6.7533 e-07 210 / 2475 M
GO:0001067 Regulatory region nucleic acid binding 6.7533 e-07 210 / 2475 M
GO:0009835 Ripening 8.4975 e-07 5 / 5 P
GO:0071695 Anatomical structure maturation 8.4975 e-07 5 / 5 P
  1. a The column ‘p-value’ indicates 1) for MGSA: the marginal value of a term being in the ‘active’ state; thus a high value gives a strong evidence for an association; the mean marginal value from 20 runs is indicated (see also Figure 3); 2) for TW: the probability of observing at least the same amount of enrichment when significant genes are randomly selected out of all genes; thus, a very small value gives strong evidence for an association.
  2. b the counts of genes in the study (x) and population (y) sets as x / y.
  3. c P, F, C refer to the three classes of the gene ontology: biological process, molecular function and cellular component respectively.
  4. Topology-Weighted (TW) and Model-based Gene Set Analysis (MGSA) results are shown.