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Filtered overlap lists were then resolved into a single table of 1 1 orthologies for all 12 species.
Computational analysis searching for transcription factors in these overlap lists revealed five and ten specific transcription factors that were up- and downregulated, respectively, following JNK inhibition (Fig. 3A and B).
Transcripts of the A and P groups from cluster only, SAM only and the cluster and SAM overlap lists were confirmed indicating that both methods of data analysis produced list of candidate genes with a low rate of false-positive results (Table S1).
When combining the overlap lists (Tables 1 and 2) from the two proteomic analysis approaches used to yield a list of proteins potentially related to a sustained productivity phenotype, twelve of these 89 proteins were found to be differentially expressed in the same direction, i.e. AKRIB8, ANXA1, ANXA4, EIF3I, G6PD, HSPA8, HSP90B1, HSPD1, NUDC, PGAM1, RUVBL1 and CNN3.
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Note that fibronectin is not on the overlap list.
The first group of genes on the overlap list is induced by Interferon α (IFNα).
This αvβ6 heterodimer activates TGF-β1, not cited in the overlap list.
KRT16 forms a heterodimer with K6, and both are strongly upregulated in the overlap list.
Further, the overlap list contains a large number of genes with a known role in inflammation.
The regulation of genes presented in the overlap list here strongly supports this theory.
Comparing these two groups, an overlap list (SI Table I) containing 261 genes was detected.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com