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

Table 3 Summary of ICAtrait linkage and Gene Ontology analyses

Trait	QTL	N	X/T	P-adj	GO over-representation
1	XII: 423789, XV: 179409	189	58/1017	< 0.001	mitochondrion
2	III: 201166	45	5/8	< 0.001	mating-type specific/mating-type specific transcriptional control
3	0	77	26/108	< 0.001	nitrogen compound biosynthesis, amine biosynthesis
4	XII: 473036	12	4/5	< 0.001	asparagine catabolism
5	0	3	NA	NA	NA
6	II: 554641	1448	54/83	< 0.001	mitochondrial ribosome
7	V: 422588	63	26/94	< 0.001	retrotransposon nucleocapsid/VLP/Virus-like particle
8	III: 90986	49	8/13	< 0.001	nitrogen compound biosynthesis, amine biosynthesis
9	X: 329085	22	4/6	< 0.001	alcohol dehydrogenase activity/alcohol dehydrogenase (NAD) activity, fermentation
10	XIV: 449639	304	225/1017	< 0.001	mitochondrion, mitochondrial ribosome
11	XII: 660992	83	22/37	< 0.001	sterol metabolism, sterol biosynthesis
12	V: 116389	9	3/13	< 0.001	pyrimidine base biosynthesis
13	XV: 563943	184	125/1017	< 0.001	oxidative phosphorylation/respiratory- chain phosphorylation, mitochondrion
14	VIII: 111686	42	16/100	< 0.001	conjugation, sexual reproduction
15	IX: 141014 XIII: 395391	8	NA	NA	NA
16	IV: 1501558, XI: 298361,	47	15/84	< 0.001	helicase activity, telomerase-independent
	XII: 824230, XII: 1056097				telomere maintenance
17	IV: 527484	6	3/3	< 0.001	sodium ion transport/sodium transport/sodium:solute transport
18	XII: 423789, XV: 179409	32	2/2	0.015	NA
19	XIII: 40447	14	4/5	< 0.001	acid phosphatase activity
20	0	63	NA	NA	NA

For each ICAtrait, we report the number and position of any significant linkages detected, the number of traits that are significantly correlated with a specific ICAtrait (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. Three of the 20 show no over-representation of biological functions while for remaining 16 both previously described and novel GO categories with associated eQTL were detected. Analysis of ICAtrait 7 and 9 are described in more detail in the text.