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Their importance in establishing developmental programs of expression is illustrated by the requirement of miRNA processing proteins like Dicer during embryogenesis [ 6], and the presence of specific miRNAs in pluripotent cells [ 7].
The proposed algorithm can be easily extended to discover e-CCC-Biclusters with time-lags, enabling the discovery of important time-lagged regulations between genes, such as activation and inhibition, as well as temporal programs of expression, in which genes are activated one by one in a predefined order.
An alternative explanation is that motifs comprised of a single TF regulating many TGs (often refereed to as SIM for single input motifs) can generate temporal programs of expression, in which TGs are activated one by one in a defined order [ 36, 37].
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Several hypotheses can be proposed to explain why pH (both PacC dependent and independent) regulation is important for mycoparasitism: pH homeostasis in the face of host-mediated changes in ambient pH, a signal provided by the host, and programming of expression of hydrolytic enzymes to be expressed near the pH optima for their activity.
T. gondii is a potent trigger for, and direct regulator of, this signaling pathway [46], [47] and its presence could upset programming of expression of these two genes, both of which have NFκB transcription factor binding sites in their promoters (Matinspector [48] and Alibaba [49] software; data not shown), during eye or brain development.
Together, these findings indicate PHOX2B∆8 proteins inhibit early LC neuronal specification, rather than the program of expression characteristic of mature LC neurons.
A shared activation program of expression changes in 191 human mφ genes was found in response to a range of bacterial pathogens, the majority of which were also activated by LPS [ 28].
We find that distinct tissue environments drive divergent programs of gene expression by differentially activating a common enhancer repertoire and by inducing the expression of divergent secondary transcription factors that collaborate with PU.1 to establish tissue-specific enhancers.
CD4+ T cells maintain flexibility in expression of genes encoding transcription factors that regulate cytokine loci, allowing adaptation to altered programs of cytokine expression in a potentially damaging inflammatory milieu [ 12].
Developmental transcription networks carry out slow and irreversible temporal programs of gene expression during development.
Embryo development is regulated by the acquisition of distinct programs of gene expression as cells differentiate.
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