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

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

GO ID	Name	P-value^a	Count^b	Ontology^c
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

^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.
^b the counts of genes in the study (x) and population (y) sets as x / y.
^c P, F, C refer to the three classes of the gene ontology: biological process, molecular function and cellular component respectively.
Topology-Weighted (TW) and Model-based Gene Set Analysis (MGSA) results are shown.

ISSN: 1471-2229