More recently, we implemented Significance Analysis of INTeractome (SAINT) within ProHits to provide scoring of interactions based on spectral counts.
Therefore, while iterating through the list of sub-maps, the following rules are implemented: Significance: if the current solution π i is labeled as a false alignment, then we stop iterating through the rest of the list.
Differential expression analysis was performed using the Bioconductor package SAMR, which implements SAM (Significance analysis of microarray) statistics in R [ 12], and a cut-off of 5% false discovery rate (FDR) was applied.
Such a data product of Swarm is not yet implemented, but its significance is known from previous studies.
This is not a problem because neither the density-based clustering algorithm, nor the non-parametric tests of significance implemented in PROC MODECLUS have distributional assumptions.
Thus, combinations of any two of the three tests were implemented here and significance of lnRH, lnRV and lnRθ' for each comparison was calculated according to standard methods [ 6, 10, 48].
We used GO::Termfinder v0.72 [25] to identify gene ontologies that were overrepresented in the generated gene lists and considered all with an False Discovery Rate (FDR <15% significant (using simulation significances implemented in GO::Termfinder).
To identify specific differentially regulated genes between CYP2S1 depleted (759) and scrambled control (SCRAM) in human bronchial epithelial cells, we used the negative binomial test of significance as implemented in the Bioconductor package DESeq with significance defined as an adjusted p-value ≤0.05 [ 27].
Compared with MCL[ 65], Affinity-Propagation[ 66], and Netwalker[ 31] that use similarity values to cluster nodes, Walktrap-GM clustering can be implemented using similarity or significance values, here we use significance scores to perform a supervised search for modules that are associated with the phenotype of interest.
When comparing the results of the two methods, statistical significance tests were performed using the suite of significance tests implemented by NIST[30].
Interactive effects on various life-history and physiological endpoints were assessed as significant deviations from the reference Independent Action (IA) model, which was implemented by testing the significance of the two-way carbaryl × parasite interaction term in two-way ANOVA's on log-transformed observational data for each clone separately.
