XB-IMG-153340
Xenbase Image ID: 153340
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EDF 10. PATHWAYS PART 2
TGF-beta pathway. Pie charts indicate the ratio of differentially expressed homeologous pairs (orange) and singleton (red). A large portion of the extracellular regulatory factors is either differentially regulated or became singleton. Genes for a type I receptor, co-receptors, an inhibitory Smad are also differentially regulated. Multicopy genes like nodal3, nodal5, and vg1 are not counted as singletons, though those S genes are deleted. Instead, these and duplicated chordin genes are categorized into differentially regulated genes.Hedgehog pathway. Upper panel: The simplified Hedgehog pathway known in Shh signalling is schematically shown. Most signalling components are encoded by both homeologous genes, whereas Hhat (shown in red) is encoded by a singleton gene. In case paralogs exist, the numbers of paralogs are shown in parenthesis. In the left cell, the Shh precursor (Hh precursor) is matured through the process involving Hhat and Hhatl, and secreted. In the right cell, the binding of Shh (Hh) to Ptch1 (Ptch) receptor inhibits Ptch1-mediated repression of Smo, leading to Smo activation and subsequent inhibition of PKA; otherwise PKA converts Gli activators to truncated repressors. As a consequence, Gli proteins activate target genes, such as Ptch1 and Hhip. The transmembrane protein Hhip binds Shh and suppresses Shh activity. Lower panel: Schematic comparison of syntenies around hhat genes of X. tropicalis chromosome 5 (top) and X. laevis 5L chromosome (middle), and the corresponding region of X. laevis 5S chromosome (bottom). The diagram is not drawn to scale.Deletions rates on L (x-axis), vs S (y-axis) for different Pfam groups. For Pfam groups we computed the number of X. laevis single-copy genes (singletons) vs homeolog pairs and computes a fraction retained. The line is expected L/S loss based on genome-wide average (56.4%). Red points show groups with high or low rates of loss (p<.01). See Supplemental Table 5 for more information.Deletions rates on L (x-axis), vs S (y-axis) for different stage WGCNA groups (visualized as a heatmap in Fig. 4a). For stage WGCNA groups we computed the number of X. laevis single-copy genes (singletons) vs homeolog pairs and computes a fraction retained. The line is expected L/S loss based on genome-wide average (56.4%). Red points show groups with high or low rates of loss (p<.01).Deletion rates on L (x-axis), vs S (y-axis) for different GO groups. For GO groups we computed the number of X. laevis single-copy genes (singletons) vs homeolog pairs and computes a fraction retained. The line is expected L/S loss based on genome-wide average (56.4%). Red points show groups with high or low rates of loss (p<0.01). See Supplemental Table 5 for more information. Image published in: Session AM et al. (2016) Image downloaded from an Open Access article in PubMed Central. Image reproduced on Xenbase with permission of the publisher and the copyright holder. Larger Image Printer Friendly View |