Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis

Table 2 Summary of Eigentrait linkage and Gene Ontology analyses

Trait	QTL	N	X/T	P-adj	GO over-representation
1	II:554641	1919	190/252	< 0.001	ribosome biogensis, rRNA processing
2	III: 90986, XV: 172654	601	92/180	< 0.001	amino acid metabolism, carbohydrate metabolism, ligase activity
3	III:201166	196	20/94	< 0.001	Ty element transposition
			4/4	< 0.001	mating pheromone activity
4	II:530481, XII:473036	13	4/5	< 0.001	asparagine catabolism, cellular response to nitrogen starvation
5	II: 554641, III: 201166	38	3/8	< 0.001	SRP-dependent cotranslational protein-membrane targeting
6	II:310928, XIV:486861	366	227/1017	< 0.001	Cellular protein/macromolecule metabolism
7	II:554641, V:116389, VIII:111686	37	6/100	0.007	conjugation, sexual reproduction, response to pheromone
8	XII: 796771, XII: 1056097	47	15/84	< 0.001	helicase activity, telomerase maintenance, mitotic recombination
9	0	74	8/106	< 0.007	Bud neck
10	XII: 660992	41	9/25	< 0.001	ergosterol/sterol/steroid/lipid metabolism/biosynthesis
11	0	8	NA	NA	Unknown
12	V:116389, XIII:379975	15	NA	NA	Unknown
13	0	8	NA	NA	Unknown
14	V:116389	8	2/13	0.039	pyrimidine base biosynthesis
15	IV:435872	5	NA	NA	Unknown
16	0	0	NA	NA	NA
17	0	0	NA	NA	NA
18	0	6	NA	NA	Unknown
19	IV:518397	5	3/3	< 0.001	sodium ion transport/sodium transport, ATPase activity
20	XV:538788	5	NA	NA	Unknown

For each eigentrait, we report the number and position of any significant linkages detected, the number of traits that are significantly correlated with a specific eigentrait (N), the number of correlated traits that have the over-represented GO attribute (X), the total number of traits that have this attribute (T) and also the over-represented GO annotation term. Two of the twenty have no correlated traits that can be called significant while six showed no significant over-representation of any biological function and remaining twelve show over-representation of certain biological functions that are consistent with previously reported trends of large scale expression variation like the mating locus, auxotrophic markers and stress response among others. Novel eQTLs detected for eigentraits 4 and 19 are described in more detail in the text.

ISSN: 1471-2105