We propose here an ORA method called protein interaction permutation analysis (PIPA) that takes advantage of literature-curated protein interactions between gene products within gene sets.
We have included these results in the main text and Figure 3B, and clarified the details in Materials and methods under "Interaction permutation analysis".
Here we present a novel ORA, protein interaction permutation analysis (PIPA), that takes advantage of canonical pathways and established protein interactions to identify pathways enriched for protein interactions connecting RNAi hits.
GO: Gene Ontology; RNAi: RNA interference; siRNA: small interfering RNA; ORA: over-representation approaches; PIPA: protein interaction permutation analysis; HPRD: human protein reference database; FAK: focal adhesion kinase; HGA: Hypergeometric enrichment analysis.
Yin-yang interaction and further permutations give rise to the five phases, which bear the full range of material and perceptual qualities and whose interaction gives rise to heaven, earth, and the myriad things, i.e., the cosmos.
This interaction leads to permutations of neutrophil function and could permit immunopathologic changes, severe disease, and opportunistic infections.
The table also shows the average number of protein-protein interactions after 10,000 permutations, and estimated p-values for getting a number of interactions after permutation that is larger than the experimental one.
> To confirm the statistical significance of the detected three-way interactions, we conducted permutations by measuring P-values of 'null data', generated in the following three manners, and comparing them with those of the interactions we detected.
Therefore, we first calculated chromosome-wise and genome-wise threshold LOD scores for the sex-by-imprinting interaction in separate permutation procedures [ 48] for each of the traits ensuring that the specific family structure in this generation was maintained.
For linear regression, we additionally examined the significance of genotype child abuse interaction effects using permutation-based procedures [Li et al., 2000; Epstein and Satten, 2003] that randomly assigned the sample BDI scores to subjects (sampled without replacement), while holding each subject's genotype and or haplotypes and environmental variables fixed.
