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But despite having a term for "term of endearment" (Kosename) Germans are way too shy with them, saving Schatz (treasure) and Mausi (little mouse) for their loved ones and ramping up the Herr and Frau for everyone else.
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As parameter settings, term-for-term analysis with Benjamini-Hochberg correction was used.
Significance of enrichment within arCOG categories was calculated using term-for-term analysis as described [ 49].
Term-for-Term analysis represents the standard method of performing statistical analysis for over-representation in GO.
The "Term-For-Term" algorithm with the Bonferroni correction for multiple testing was chosen in the calculations.
First, we tested for statistical enrichment of genes with particular Gene Ontology functional annotations [ 73], using ONTOLOGIZER version 2.0 [ 74], with the "Term-for-Term" calculation method and Bonferroni-corrected P < 0.05.
Six enrichment calculation methods are available in the current version of POEAS: Model-Based Gene-Set Enrichment Analyses (MGSA), 32 Parent Child-Intersection, Parent Child-Intersectionrm-For-Term, 13 ToParent Child-UnionoParent Child-Union
GO analyses were realised using the Ontologizer tool (http://compbio.charite.de/index.php/ontologizer2.html), performing term-for-term hypergeometric testing with the Benjamini and Hochberg false discovery rate correction, or a Bayesian modelling approach using the model-based gene set analysis (MGSA) option [ 84].
For each tissue, the actively expressed genes were used as the population gene set in term-for-term comparisons with each of the sex-biased expression categories as separate study sets (absolute fold change > 1, p adj < 0.05 cutoffs to denote sex-bias).
6, 17, 35 This list of 700 TAIR locus IDs was used as input, and the multiple-testing correction method was set to "Bonferroni," the enrichment calculation method was set to "Term-For-Term," and the resampling steps were set to "1000".
In the gene ontology analysis (Additional files 5, 6, 7, 8, 9, 10 and 11), the GO term for acyl carrier activity was prominent in the lists from the term-for-term and MGSA analysis of genes induced by vancomycin or bacitracin in the 90 min sample, with as many as 8 genes associated with this term present in the lists of up-regulated genes.
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