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In the hypothesis generation phase, each gene was assigned to a single GO ID in the biological function category; when a gene is assigned to multiple categories (as is generally the case), it was instead assigned only to the category that was closest to containing exactly 125 genes (with ties broken for smaller categories, so a GO ID with 100 genes would be preferred to a GO ID with 150).
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A key step in any outbreak investigation is the hypothesis-generation phase (3 ).
These data sets were used only in the hypothesis-generation phase.
The value of descriptive epidemiology, extensive environmental investigation, and the hypothesis-generation phase cannot be overemphasized.
Robust descriptive epidemiology, a thorough environmental investigation, and the hypothesis-generation phase become even more essential.
GO categories and other measures individually identified in the hypothesis-generation phase are tested as a group in the hypothesis-testing phase.
In the statistical tests of this hypothesis-generation phase, other measures of positive selection where either not strong predictors of eQTLs; or, attempts to utilize measures other than H|H failed because the statistical models did not converge.
Of these, ΔDAF[ 30], |ΔDAF|[ 30], ΔiHH[ 17], Fst [ 31], and iHS[ 17], along with minor allele frequency (MAF) were used in at least one model in the hypothesis-generation phase.
In the first (hypothesis-generation) phase, seven modestly-powered QTL data sets from either Lymphoblastic Cell Lines (LCLs), Monocytes or human liver [ 20- 25] are used to pick prediction variables, and, categories of genes in which positive selection scores differentiate cis-eQTLs from the surrounding gene.
This confirms the biological findings outlined in the previous section, although Group 1 eQTLs shows no association with H|H at all (rather than a negative association) and the association in Group 2 is somewhat smaller than it was in the hypothesis-generation phase data.
Further, this hypothesis generation itself generates discoveries that might lead to their own hypotheses.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com