Fig. 3. The most highly affected pathways and functions in mutant cumulus cells. The 744 transcripts that were commonly changed in all three pairwise comparisons of cumulus transcriptomes in WT, Bmp15^-/-, and DM mice were uploaded into the IPA platform, and canonical pathways and molecular functions analyses were carried out using Ingenuity Pathways Knowledge Base as reference dataset. (A) All canonical pathways identified that were significantly affected. (B) The 10 most affected molecular functions. The orange vertical line crossing all the bars in A and B indicates the threshold of significance (P=0.05), and bars above this line have a P-value of less than 0.05. (C) GenMAPP display of transcripts encoding enzymes required for cholesterol biosynthesis pathway. The list of all the genes on the array was uploaded into GenMAPP, and significantly downregulated transcripts were defined by the criteria of FC (fold change) <-1 and Fs P<0.01 in all three pairwise comparison analyses, and are shown in orange boxes. Upregulated transcripts are defined by the criteria of FC>1 and Fs P<0.01 in all three pairwise comparison analyses. No transcripts are identified to be upregulated by these criteria. Dotted boxes indicate that the transcripts in these boxes are represented by >1 probe set. The FC of each transcript is listed on the right side of the corresponding box. Only the FC_{DM vs WT} of each transcript is shown here owing to space limitation. Minor modification of the original MAPP in GenMAPP was made here in order to cover most of the key enzymatic steps in this pathway, such as steps for producing FF-MAS and T-MAS. Panel C, by Michael Lieberman and Ned Mantei (2004), is reproduced from GenMAPP.