We performed multiple comparisons in analyzing our data without adjustment, increasing the likelihood of false-positive associations.
Finally, it should be noted that Geomfinder is not intended for simultaneous multiple comparisons in a large number or families of proteins.
We did not consider adjustment for multiple comparisons in this exploratory, hypothesis-generating set of analyses.
Moreover, the use of correction for multiple comparisons in this area is debated [45].
The level of statistical significant (p value) was set to 10−5 to allow for multiple comparisons in gene networks.
To account for multiple comparisons in paired t tests, we applied a manual Bonferroni correction (P-values×number of comparisons).
Tukey's method or Dunnett method was used to adjust p-values due to multiple comparisons in ANOVA analysis.
For all multiple comparisons in which statistical significance is reported, ANOVA values were significant to 0.05 or lower.
Data were analyzed using the Student's t-test or ANOVA with Tukey-Kramer multiple comparisons in the Statcel2 (the add-in forms on Excel (Microsoft)) software.
We identified these areas using a conjunction analysis (intersection of areas significantly correlated at p<0.001, uncorrected for multiple comparisons, in each instance, [27]).
One-way analysis of variance (ANOVA) combined with the Tukey post hoc test of means were used for multiple comparisons in cell culture experiments.
