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Incorporating the actual growth conditions when inferring regulatory relationships provides detailed insight in the functionality of the TFs that are triggered by changes in the employed cultivation conditions . As a first proof of the method 's effectiveness , and in order to empirically determine a reasonable default cutoff for obtaining the final list of candidates , we analyzed whether genes with the highest ranks in the single organism lists are actually enriched of orthologous sequences . The Cornell Institutional Animal Care and Use Committee approved the care of animals and the Association for Assessment and Accreditation of Laboratory Animal Care ( AAALAC ) approved the facility . The diamond and square markers represent the mismatch with and without the regularization constraint . In the hours subsequent to this , cell proliferation is initiated ; this last process is also modulated by Pax6 and the role of Pax6 in this regard has been studied previously [ 64 ] . The default iHOP gene-focused Web page without the enhancements provided by the iHOPerator script . These findings may simply mean that any requirement for activation of the Ras pathway in Wnt1-induced tumors may be satisfied by some other means , such as other oncogenic mutations ; this issue is further addressed in a later section . Numbers on the branches indicate the percentages of bootstrap support derived from a heuristic search with 100 random addition replicates ; this search included a tree-bisection-reconnection branch-swapping algorithm .