Skip to main content

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).