Data were analyzed in the "Functional Annotation Clustering" tool using the "High" classification stringency setting for Molecular Function (MF) and Biological Process (BP) Gene Ontology (GO) terms.
Curves can be obtained by increasing the temperature or decreasing the cation concentration and studying the change in signal as a function of changed stringency.
They are formed at virtually any taxonomic level or function, regardless of the stringency of the parameters and the existence of reads of bacterial origin in the dataset.
Moreover, we purposely chose a low cutting height of 0.99 (default in WGCNA R package is 0.995) while implementing the dynamic tree cut method of the blockwiseModules function, to increase the stringency of the module detection step.
This language, together with the idea of "comparative stringency," ineluctably suggests the idea that the mapping function might be the same in each case of conflict and that it might be a quantitative one.
"Functional Annotation Clustering" with default classification stringency is applied to derive all the related functions associating with their enrichment scores and P-values.
DAVID was run using the high stringency setting and the following annotation groups: Molecular Function level 4 5, Cellular Component level 4 5, Biological Function level 4 5, InterPro terms, and PIR keywords.
Finally, the 'keyset to functionction was used and the stringency was adjusted to 1e−25 with a minimum of 2 ends matching.
The eight groups listed in Table 1 were extracted with the highest clustering stringency, using the built-in gene classification function in the Database for Annotation, Visualization and Integrated Discovery (DAVID, http://david.abcc.ncifcrf.gov) bioinformatics resources [16], [17].
Ideally, melting curves should be generated for each probe on an array during assay development to determine whether the probes can function together at a given stringency (temperature and buffer composition).
