Next-generation text-mining mediated generation of chemical response-specific gene sets for interpretation of gene expression data

Kristina M Hettne; André Boorsma; Dorien A M van Dartel; Jelle J Goeman; Esther de Jong; Aldert H Piersma; Rob H Stierum; Jos C Kleinjans; Jan A Kors

doi:10.1186/1755-8794-6-2

Table 4 The top 25 embryonic structure gene sets

From: Next-generation text-mining mediated generation of chemical response-specific gene sets for interpretation of gene expression data

Embryonic structure	p-value	WEC effect
neural plate and or tube	1.5e-07	Posterior neuropore open
second branchial arch structure	4.9e-06	Branchial bars deformed
fourth branchial arch structure	4.9e-06	Branchial bars deformed
entire fourth branchial arch	4.9e-06	Branchial bars deformed
structure of first pharyngeal pouch	6.3e-06	Otic vesicles deformed
entire first pharyngeal pouch	6.3e-06	Otic vesicles deformed
entire neural tube	6.4e-06	Posterior neuropore open
Branchial Region	7.3e-06	Branchial bars deformed
entire second branchial arch	7.3e-06	Branchial bars deformed
structure of tympanic annulus	7.3e-06	Otic vesicles deformed
entire tympanic annulus	7.3e-06	Otic vesicles deformed
Neuroectoderm	7.5e-06	Posterior neuropore open
entire cloacal membrane	9.8e-06	No corresponding scoring parameter available in the WEC.
branchial arch structure	1.1e-05	Branchial bars deformed
structure of cloacal membrane	1.1e-05	No corresponding scoring parameter available in the WEC.
entire ostium secundum	1.1e-05	Heart ventrally turned
structure of third aortic arch	1.1e-05	Heart ventrally turned
entire branchial arch	2.2e-05	Branchial bars deformed
Otic Vesicle	2.2e-05	Otic vesicles deformed
entire auditory vesicle	2.2e-05	Otic vesicles deformed
structure of embryo stage 6	2.2e-05	No corresponding scoring parameter available in the WEC.
structure of early somite stage	2.2e-05	Somites irregular
entire early somite stage	2.2e-05	Somites irregular
third branchial arch structure	2.2e-05	Branchial bars deformed
entire third branchial arch	2.2e-05	Branchial bars deformed

False discovery rate-corrected p-values for the top 25 embryonic structure gene sets from the weighted global test on triazole gene expression data from the embryonic stem cell test, together with the effect seen in rat postimplantation Whole Embryo Culture (WEC).

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