Gene transcription or gene expression is one of the most important processes in cellular response to internal and external stimuli. Therefore, this is a highly regulated process by specific proteins called transcription factors and transcriptional regulators. Transcription factors (TFs) are proteins that bind to specific cis-elements in the promoters of genes to activate or repress their transcription directly. In contrast, transcriptional regulators (TRs) are proteins that although involved in gene expression control do not bind independently to gene promoters. Transcriptional regulators modulate gene expression by interacting with transcriptions factors, remodeling chromatin or other indirect mechanisms.
In ChlamyNET we identified 118 different transcription factors (TFs) classified into 28 different families according to their sequence similarity. The distribution of the TFs over the clusters of ChlamyNET is not uniform. The blue and red clusters are enriched with TFs, figure (A) below. In ChlamyNET we identified 109 different transcriptional regulators (TRs) classified into 17 different families according to their sequence similarity. The distribution of the TRs over ChlamyNET is uniform, figure (B) below.
In ChlamyNET, instead of classifying TFs and TRs based on their sequence similarity, we have classified them according to their co-expression patterns. We applied clustering techniques based on the correlation between their expression profiles to identify thirteen different groups of TFs and TRs that, potentially, exert their function over target genes in a coordinated fashion. Using GO term enrichment over the genes directly linked to each group of TFs and TRs we determined the biological processes potentially regulated by them. Finally, we performed transcriptional factor binding site (TFBS) enrichment analysis over the promoters of genes directly linked to each group of TFs and TRs in order to identify the cis-elements responsible for the coordinated regulation. In what follows you can find detailed information about the analysis of each group of TFs and TRs: