Reprogramming of 3′ Untranslated Regions of mRNAs by Alternative Polyadenylation in Generation of Pluripotent Stem Cells from Different Cell Types (original) (raw)
Figure 5
Gene expression analysis in generation of iPS cells.
(A) Correlation between mRNA expression of 94 poly(A) genes and nRUD values for all cell types, including before and after reprogramming and partially reprogrammed cells. Poly(A) genes are those reported in [21] plus gene encoding Clp1 (see Table S3 for the complete list). (B) A list of genes encoding core polyadenylation factors that are consistently regulated in generation of iPS cells. Fold changes (ratio of after reprogramming to before reprogramming) are shown in a heatmap according to the color scale shown at the bottom. Only the genes with consistent trend of regulation, either upregulation or downregulation in >9 out of 10 data sets, during reprogramming of somatic cells are shown. Data for SC and different tissues in embryonic development are also shown for comparison. Human gene symbols are used to annotate genes. (C) Gene Ontology (GO) terms that are significantly associated with genes upregulated (top) and downregulated (bottom) during generation of human and mouse iPS cells from somatic cells. Significance score (SS) is used to represent _P_-values (see Methods for detail), and is shown in a heatmap according to the scale shown in the graph. The poly(A) gene group was also analyzed and is shown in the middle. Its _P_-values are <0.01 for all cell types. The median SS based on reprogramming of somatic cells is listed and used to sort GO terms. GO terms associated with more than 1,500 genes are considered too generic and are discarded. To eliminate redundancy, we require that the reported GO terms do not overlap with any other GO term with greater SS by more than 25% of associated genes.