Living cells are constantly responding to internal and external signals. From the simplest yeast that adapts to changes in temperature, to a stem cell in the human body that decides to which type of cell to differentiate. A major part of the cellular response to signals is production of proteins according to the cell’s needs. The first step in protein production is transcription of genes to intermediate mRNA molecules, from which the proteins are translated. In the past decade, technological developments enabled measuring of mRNA expression levels of all the genes in the cell, providing a profile of cellular expression at a given time point. Comparison of such profiles under different conditions (e.g., before and after a drug treatment) provides a useful insight into which proteins play a role in these conditions (e.g., in response to the drug). Gene transcription is tightly regulated by a complex multilayer mechanism. An important part of this mechanism are transcription factors proteins that bind the DNA and activate or repress transcription. The binding of transcriptio
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