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The activation of NFκB was also reported in this mouse model [ 29, 30], but the enrichment of bindings sites for NFAT and other transcription factors in the list of genes that are differentially expressed suggests that molecular networks regulated by these factors may be important for the pathogenesis of disease.
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Assessment for functional enrichment of "developmental transcription factor" in the list of LUAT-associated coding genes was performed using R and TBrowser database [ 78].
In addition, promoter analysis identified ISRE as the top enriched transcription factor motif in the list of differentially expressed genes (q < 0.05).
A hypergeometric enrichment test was performed to identify over-represented transcription factor interactions in the list of reactions from each comparison passing the cutoff P > 0.9 based on known transcription factor-gene interactions [ 24].
To assess the significance of over-represented GO terms or the transcription factor families in the list of the regulated genes against the genome, Fisher's Exact Test (p < 0.01) [ 86] and Benjamini and Hochberg method (FDR < 0.05) [ 79] were used.
Other important regulatory factors are included in the list of Transformation-Regulated genes.
All three splicing factors were present in the list of predicted FBF-2 cofactors.
However, in this study no predicted sigma-70 factors were identified in the list of genes containing a putative A. baumannii FUR binding site (Additional file 2).
To ensure all risk factors were included in the list of the FWB, a global literature review was performed using the search terms 'neonatal hearing loss' and 'postnatal hearing loss'.
A score for each transcription factor is given by a p-value that denotes the overrepresentation of the given transcription factor targeted genes in the list of up-regulated genes relative to the regulations of that transcription factor targeted genes in the whole Yeastract database We have shown that depletion of Pkh triggers a heat stress-like transcriptional response.
On the other hand, none antiviral factor was identified in the list of 8 genes down-regulated during infection.
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