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Herein, a systems biology approach was developed to identify the components and role of cross-talk between nitrate and hormone signals, likely to be involved in the conditional response of NO<jats:sub>3<\/jats:sub>\n              <jats:sup>-<\/jats:sup> signaling.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Biclustering was used to identify a set of genes that are N-responsive across a range of Nitrogen (N)-treatment backgrounds (i.e. nitrogen treatments under different growth conditions) using a meta-dataset of 76 Affymetrix ATH1 chips from 5 different laboratories. Twenty-one biclusters were found to be N-responsive across subsets of this meta-dataset. <jats:italic>N-bicluster 9<\/jats:italic> (126 genes) was selected for further analysis, as it was shown to be reproducibly responsive to NO<jats:sub>3<\/jats:sub>\n              <jats:sup>-<\/jats:sup> as a signal, across a wide-variety of background conditions and datasets. <jats:italic>N-bicluster 9<\/jats:italic> genes were then used as \"seed\" to identify putative cross-talk mechanisms between nitrate and hormone signaling. For this, the 126 nitrate-regulated genes in <jats:italic>N-bicluster 9<\/jats:italic> were biclustered over a meta-dataset of 278 ATH1 chips spanning a variety of hormone treatments. This analysis divided the bicluster 9 genes into two classes: i) genes controlled by NO<jats:sub>3<\/jats:sub>\n              <jats:sup>-<\/jats:sup> only <jats:italic>vs<\/jats:italic>. ii) genes controlled by <jats:italic>both<\/jats:italic> NO<jats:sub>3<\/jats:sub>\n              <jats:sup>-<\/jats:sup> and hormones. The genes in the latter group showed a NO<jats:sub>3<\/jats:sub>\n              <jats:sup>-<\/jats:sup> response that is significantly enhanced, compared to the former. <jats:italic>In silico<\/jats:italic> analysis identified two Cis-Regulatory Elements candidates (CRE) (E2F, HSE) potentially involved the interplay between NO<jats:sub>3<\/jats:sub>\n              <jats:sup>-<\/jats:sup> and hormonal signals.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>This systems analysis enabled us to derive a hypothesis in which hormone signals are proposed to enhance the nitrate response, providing a potential mechanistic explanation for the link between nitrate signaling and the control of plant development.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1752-0509-3-59","type":"journal-article","created":{"date-parts":[[2009,6,6]],"date-time":"2009-06-06T18:21:03Z","timestamp":1244312463000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":48,"title":["A system biology approach highlights a hormonal enhancer effect on regulation of genes in a nitrate responsive \"biomodule\""],"prefix":"10.1186","volume":"3","author":[{"given":"Damion","family":"Nero","sequence":"first","affiliation":[]},{"given":"Gabriel","family":"Krouk","sequence":"additional","affiliation":[]},{"given":"Daniel","family":"Tranchina","sequence":"additional","affiliation":[]},{"given":"Gloria M","family":"Coruzzi","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2009,6,6]]},"reference":[{"issue":"10","key":"327_CR1","doi-asserted-by":"publisher","first-page":"389","DOI":"10.1016\/S1360-1385(98)01311-9","volume":"3","author":"NM Crawford","year":"1998","unstructured":"Crawford NM, Glass ADM: Molecular and physiological aspects of nitrate uptake in plants. 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