Fig. 5
Wnt, SHH, and BMP pathways in fibropapillomatosis tumors. a Left: Activation/inhibition z-scores of Wnt- and SHH-related IPA pathway analysis findings of the fibropapillomatosis tumor differentially expressed transcripts (RNA-seq), p-values calculated by right-tailed Fisher’s Exact Test, with Benjamini–Hochberg correction. Right: Interaction map of the 43 Wnt, SHH, and BMP pathway component and target genes differentially expressed in fibropapillomatosis tumors (RNA-seq). Image generated using GeneMANIA (v3.5.0, http://genemania.org/)104. In addition to the 43 DE genes (nodes with stripped shading), 20 closely functionally-related network components are also shown (nodes with uniform shading). Basal Cell Carcinoma KEGG pathway score of the DE components of the network is shown below the network. b Fold change in expression of the differentially expressed transcripts (RNA-seq) of Wnt, SHH, and BMP pathway-related genes. When more than one transcript of a gene was present in the top 600 DE genes (300 per direction), each transcript is denoted by t1, t2, t3, etc. Differential expression p-values reported are adjusted p-values, generated by DESeq2, by a Wald test followed by Benjamini–Hochberg correction. Transcript expression values underlying the differential expression analysis are provided in Supplementary Table 4. c Relative expression of Wnt5a mRNA in a panel fibropapillomatosis tumor and control samples, as detected by RT-qPCR. Data for 66 tumor samples and 13 control samples. The p-value was calculated by t-test
