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Table 3 Comparison of the PQIs (Kruskal-Wallis Rank Sum Tests). See Additional files 2, Additional files 3, Additional files 4, Additional files 5, Additional files 6, Additional files 7 and 8 for the corresponding boxplots.

From: Combining evidence, biomedical literature and statistical dependence: new insights for functional annotation of gene sets

  Null hypotheses
  GOAPUB ≠ GOA GOAPUB ≠ PUB +Dep. ≠ +Random
Clusters χ2 p-value χ2 p-value χ2 p-value
Iron metabolism:       
Down 48.9203 *** 41.2014 *** 255.7346 ***
Up 27.1614 *** 41.1756 *** 73.0033 ***
Glioblastomas:       
glioGBM 29.7468 *** 1.1743 ns 85.9769 ***
glioPRIM 62.7100 *** 90.2077 *** 97.2004 ***
glioSEC 0.6282 ns 1.5421 ns 76.2122 ***
Circadian Rhythms:       
circ 53.1073 *** 26.2437 *** 126.8363 ***
Human fetal lung:       
lung 19.0615 *** 36.1988 *** 16.3595 ***
Human retinal pigment epithelium:       
arpe19 3.999 * 9.5254 * 42.7507 ***
rpe 21.2666 *** 30.0108 *** 105.1405 ***
Alzeimers disease:       
alzheimer 121.7634 *** 151.0647 *** 14.2819 ***
Acute lymphoblastic leukemias:       
bcr-abl 41.6444 *** 44.5055 *** 137.2054 ***
hyperdiploid 14.0618 *** 22.3200 *** 137.0784 ***
novel 21.1505 *** 91.1497 *** 22.9347 ***
tel-aml1 15.5670 *** 6.5539 ns 118.602 ***
  1. † Null hypotheses: comparison of the PQIs between Evidence (GOA) and a combination of Evidence and Literature (GOAPUB ≠ GOA). Comparison of the PQIs between Literature (PUB) and a combination of Evidence and Literature (GOAPUB ≠ PUB). Comparison of the PQIs between the combination of Evidence and Literature enriched with the associative relations (+Dep.) or a random term set of the same size (+Random).
  2. ‡ p-value: ≤ 0.01 (***) ; ≤ 0.05 (*) ; non-significant (ns).