biostudies-literatureUnknown3(2)Fehrmann RSIt has been hypothesized that the net expression of a gene is determined by the combined effects of various transcriptional system regulators (TSRs). However, characterizing the complexity of regulation of the transcriptome is a major challenge. Principal component analysis on 17,550 heterogeneous human microarray experiments revealed that 50 orthogonal factors (hereafter called TSRs) are able to capture 64% of the variability in expression in a wide range of experimental conditions and tissues. We identified gene clusters controlled in the same direction and show that gene expression can be conceptualized as a process influenced by a fairly limited set of TSRs. Furthermore, TSRs can be linked to biological functions, as we demonstrate a strong relation between TSR-related gene clusters anPloS onee1656https://www.ebi.ac.uk/biostudies/studies/S-EPMC2250855biostudies-literatureA new perspective on transcriptional system regulation (TSR): towards TSR profiling.PMC2250855de Bont ESvan der Zee AGKamps WATer Elst AFehrmann RSWeidenaar ACde Jonge HJde Vries ACrijns AGHofstra RMTe Meerman GJGerbens Fde Jong Sde Vries EGfalseA new perspective on transcriptional system regulation (TSR): towards TSR profiling.It has been hypothesized that the net expression of a gene is determined by the combined effects of various transcriptional system regulators (TSRs). However, characterizing the complexity of regulation of the transcriptome is a major challenge. Principal component analysis on 17,550 heterogeneous human microarray experiments revealed that 50 orthogonal factors (hereafter called TSRs) are able to capture 64% of the variability in expression in a wide range of experimental conditions and tissues. We identified gene clusters controlled in the same direction and show that gene expression can be conceptualized as a process influenced by a fairly limited set of TSRs. Furthermore, TSRs can be linked to biological functions, as we demonstrate a strong relation between TSR-related gene clusters an2008-01-01T00:00:00Z2008 Feb2025-04-26T19:56:12.142Z2019-03-26T23:01:31ZS-EPMC22508551829713610.1371/journal.pone.0001656