In the Fisher exact test invoked in DAVID [ 16] to identify enriched pathways, the proportion of genes submitted must be significantly greater than the proportion of genes found by chance.
Haplogroups associated with longevity were identified as those with a larger proportion of enriched patterns out of the total number of patterns associated with the haplogroup.
The number of tissue-enriched contigs and the proportion of contigs annotated in the GigasDatabase are shown in Table 1. Figure 3B shows the heat map of the tissue-enriched contigs, and the complete list with their descriptions are given in Additional file 5.
Examining all categories defined by the generic GO Slim subsets of biological processes, molecular functions, and cellular components confirms this difference among processes and functions whereas components instead exhibit similar proportions of enriched terms in the three lineages (supplementary table 5 and fig. 8, Supplementary Material online).
The idea is essentially to allow a proportion p21 of non-enriched probes in an enriched region and a proportion p12 of enriched probes in a non-enriched region.
Old groundwater with enriched 13C indicates the higher proportion of C4 species in the late Pleistocene.
As the zebrafish is not a close relative to our catfish and because the sequences of interest display high sequence divergence, a substantial proportion of the enriched library yielded no significant Blast matches.
We performed susceptibility testing by using an agar proportion method on enriched Middlebrook 7H10 medium (BBL Microbiology Systems, Cockeysville, MD, USA) at the following concentrations: rifampicin 1 μg/mL, isoniazid 0.2 μg/mL, streptomycin 2 μg/mL and 10 μg/mL, and ethambutol 5 μg/mL.
Susceptibility testing was performed using standard agar proportion method on enriched Middle brook 7H10 medium (BBL) at the following final drug concentrations; rifampicin 1 ug/ml and 5 ug/ml, isoniazid 0.2 ug/ml and 1 ug/ml, streptomycin 2 ug/ml and 10 ug/ml and ethambutol 5 ug/ml and 10 ug/ml, ethionamide 5 ug/ml, capreomycin 10 ug/ml, cycloserine 30 ug/ml and ciprofloxacin 2 ug/ml.
