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The BMP pathway was differentially activated with early treadmill training as shown by Ingenuity Pathway Analysis.
Ingenuity Pathway Analysis results support several possibilities for ZAP70/Syk activation as a consequence of pathways activated by AF (Supplementary Figure S4).
Of the 16 Ox-E/ER genes involved in the second highest scoring network identified by Ingenuity, nine show a coordinated expression pattern signifying activated TNF signaling.
Ingenuity® predicted that nine upstream transcriptional regulators were activated (TP53, CD24, NUPR1, CDKN1A) or inhibited (FOXM1, FLI1, MYC, CSF2, CCDN1) in resistant cell lines (P <0.01).
Relationships were examined manually in the Ingenuity Pathways Knowledge Base to determine if target genes were activated or repressed by p53.
To identify signaling pathways activated by retroviral insertions, we took the 346 candidate target genes and used Ingenuity Pathway Analysis software to investigate whether these genes play a role in canonical signaling pathways.
We conducted a genome-wide analysis utilising an Ingenuity Pathway Analysis algorithm to address if any known toxicity pathway(s) were activated or induced after treatment with ETP-45658 (or by the reference compound PI-103).
To identify biological pathways that were activated or attenuated by Ptf1a deletion, we analyzed this RNA-seq data set using Qiagen's Ingenuity Pathway Analysis (IPA, QIAGEN Redwood City, www.ingenuity.com) (Thomas and Bonchev, 2010; Kramer et al., 2014).
Ingenuity pathway analyses to identify affected functional and canonical pathways showed that SARM-1, SARM-2 and DHT activated overlapping but distinct miRs and consequently gene networks, but with varying efficacy (Fig. 2C).
