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Table 2 Summary of Eigentrait linkage and Gene Ontology analyses

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

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
  1. 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.