To understand the functions of the commonly regulated genes, we identified most significantly functional categories using the Ingenuity function analysis tool (Ingenuity Systems, Inc., Redwood City, CA).
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Among the transcripts up-regulated in the tumour samples, 54 were found eligible for Ingenuity function and pathway analysis.
Ingenuity function analysis of the 4,163 progenitor-specific up-regulated transcripts, however, revealed broad ontologies, such as "Cellular Growth and Proliferation", "Hematologic Disease" and "Oncogenicity", without prioritization of lineage-specific pathways (Figure 1D).
Ingenuity functional analysis identified biological functions and/or diseases that were most significant enriched and generated p-value to determine the probability that each biological function assigned to that data set was due to chance alone.
The three functional genomic approaches included: Ingenuity® Functions, Diseases and Canonical Pathways Analysis: Functional analysis was done with Ingenuity® Pathways Analysis (Ingenuity® Systems, www.ingenuity.com, Application version 8.6, Content version 3003).
First, the Ingenuity® functions, GO terms and gene sets found from the expression data confirm and are confirmed by studies done long ago with very different methodologies.
The Ingenuity® functions unique to Week 20 are summarized in Table 4 and the Ingenuity® diseases unique to Week 20 in Table 5; the complete unabridged data is provided in Table S2.
Ingenuity biological function analysis revealed that completely different repertoires of molecules are recruited to exert the same biological functions in neuronal differentiation.
Ingenuity Biological Function analysis identified categories such as 'cancer' and 'reproductive system disease' as expected (Supplementary Table S4).
Significantly altered Ingenuity biological function categories included development, immune response, and cell proliferation [see Supplemental Material, Table 2 (http://dx.doi.org/10.1289/ehp.1104018)].
