title: Dynamic changes in subgraph preference profiles of crucial transcription factors.
abstract: Transcription factors with a large number of target genes--transcription hub(s), or THub(s)--are usually crucial components of the regulatory system of a cell, and the different patterns through which they transfer the transcriptional signal to downstream cascades are of great interest. By profiling normalized abundances (A(N)) of basic regulatory patterns of individual THubs in the yeast Saccharomyces cerevisiae transcriptional regulation network under five different cellular states and environmental conditions, we have investigated their preferences for different basic regulatory patterns. Subgraph-normalized abundances downstream of individual THubs often differ significantly from that of the network as a whole, and conversely, certain over-represented subgraphs are not preferred by any THub. The THub preferences changed substantially when the cellular or environmental conditions changed. This switching of regulatory pattern preferences suggests that a change in conditions does not only elicit a change in response by the regulatory network, but also a change in the mechanisms by which the response is mediated. The THub subgraph preference profile thus provides a novel tool for description of the structure and organization between the large-scale exponents and local regulatory patterns.
authors.affiliation: Bioinformatics Laboratory and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Zhihua
authors.initials: Z
authors.lastname: Zhang
authors.forename: Changning
authors.initials: C
authors.lastname: Liu
authors.forename: Geir
authors.initials: G
authors.lastname: Skogerbø
authors.forename: Xiaopeng
authors.initials: X
authors.lastname: Zhu
authors.forename: Hongchao
authors.initials: H
authors.lastname: Lu
authors.forename: Lan
authors.initials: L
authors.lastname: Chen
authors.forename: Baochen
authors.initials: B
authors.lastname: Shi
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.forename: Jie
authors.initials: J
authors.lastname: Wang
authors.forename: Tao
authors.initials: T
authors.lastname: Wu
authors.forename: Runsheng
authors.initials: R
authors.lastname: Chen
mesh_terms: D002453:Cell Cycle; D015966:Gene Expression Regulation, Fungal / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000166:cytology / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism*; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D014157:Transcription Factors