Open AccessDynamic Changes in Subgraph Preference Profiles of Crucial Transcription Factors
Author(s) -
Zhihua Zhang,
Changning Liu,
Geir Skogerbø,
Xiaopeng Zhu,
Hongchao Lu,
Lan Chen,
Baochen Shi,
Yong Zhang,
Jie Wang,
Tao Wu,
Runsheng Chen
Publication year - 2006
Publication title -
plos computational biology/plos computational biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.628
H-Index - 182
eISSN - 1553-7358
pISSN - 1553-734X
DOI - 10.1371/journal.pcbi.0020047
Subject(s) - saccharomyces cerevisiae , gene regulatory network , biology , transcription factor , computational biology , regulation of gene expression , gene , genetics , gene expression
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.