Fig. 1

Analysis of gene expression. Principal component analysis of gene expression inferred from human (a), mouse (b) and chimpanzee (c) RNA-Seq libraries. x and y axes correspond to the first and second principal components. Axis labels indicate the amount of variance explained. Colors correspond to cell types (see below for abbreviations), while symbols indicate the individual studies from which the data sets were derived (see also Table 1). (d and e) Gene set enrichment analyses of genes that were differential gene expression in reprogrammed cells relative to their parental somatic cells. The significance (log10 false discovery rates (FDR) of enrichments in either differentially expressed genes (d) or in genes with increased expression (“upregulated”) during iPSC formation (e) relative to all expressed genes are shown as heatmaps. GO terms are shown in rows and specific comparisons (data sets) are shown in columns. The organisms from which individual data sets were derived are indicated by the color in the bar above the heatmaps: human - blue; mouse - red; chimpanzee - purple. For clarity, values of log10 FDR were capped at -50. Column dendrograms are based on complete linkage clustering with Euclidean distances. Column (x axis) labels indicate the data sets that were compared, using a 1-letter code that maps to the corresponding Sequence Read Archive accession (see legend above (d) and (e), right side). Abbreviations are: APC, adipose progenitor cells; ciPSC, chemically induced pluripotent stem cells; FB, fibroblasts; iPSC, induced pluripotent stem cells; hiF, human inducible fibroblast-like cells; HPC, hematopoietic progenitor cells; LB, lymphoblastoid cells; MEF, mouse embryonic fibroblasts; SSC, spermatogonial stem cells. hiF-T cells constitutively express human TERT (telomerase reverse transcriptase). See Table 1, Table S2 and the original references for details on specific studies