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. Author manuscript; available in PMC: 2022 Mar 12.
Published in final edited form as: Cell Rep. 2022 Feb 15;38(7):110364. doi: 10.1016/j.celrep.2022.110364

Figure 2. RNA-seq SOM metaclustering reveals developmental gene modules that contain similarly regulated genes.

Figure 2.

(A) SOM slices relating to gene expression signal Wildtype at stage 10.5 and the fold change between Foxh1 MO and control experiments at stage 10.5. Creation of SOM visualization is described in STAR Methods. Metaclusters containing genes from the core ME network show unique temporal dynamics during development. nodal, nodal2, and sia are grouped left and gsc, nodal1, lhx, and osr2 are grouped right (top). Overlaid metacluster boundaries show the genes that are up- and down-regulated upon Foxh1 MO KD (bottom).

(B) Each metacluster is filled with genes with a similar expression profile (labeled “Eigen-Profile”); for example, a heatmap of the genes in metacluster 11 is shown.

(C) Heatmap of average temporal expression profiles of genes belonging to 13 RNA metaclusters. Parentheses after RNA metaclusters indicate number of genes in each RNA metacluster.

(D) Two-tailed Wilcox hypothesis analysis applied on gene metaclusters. Each metacluster responded to each MO experiment differently at different time points.

(E) GO term enrichments for genes within three example RNA SOM metaclusters. Each metacluster had unique functional enrichments supporting the coherence of these clusters.

See Figure S1.