{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,5]],"date-time":"2023-01-05T14:32:40Z","timestamp":1672929160982},"reference-count":51,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2009,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Network Component Analysis (NCA) is a network structure-driven framework for deducing regulatory signal dynamics. In contrast to principal component analysis, which can be employed to select the high-variance genes, NCA makes use of the connectivity structure from transcriptional regulatory networks to infer dynamics of transcription factor activities. Using the budding yeast <jats:italic>Saccharomyces cerevisiae<\/jats:italic> as a model system, we aim to deduce regulatory actions of cytokinesis-related genes, using precise spatial proximity (midbody) and\/or temporal synchronicity (cytokinesis) to avoid full-scale computation from genome-wide databases.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>NCA was applied to infer regulatory actions of transcription factor activity from microarray data and partial transcription factor-gene connectivity information for cytokinesis-related genes, which were a subset of genome-wide datasets. No literature has so far discussed the inferred results through NCA are independent of the scale of the gene expression dataset. To avoid full-scale computation from genome-wide databases, four cytokinesis-related gene cases were selected for NCA by running computational analysis over the transcription factor database to confirm the approach being scale-free. The inferred dynamics of transcription factor activity through NCA were independent of the scale of the data matrix selected from the four cytokinesis-related gene sets. Moreover, the inferred regulatory actions were nearly identical to published observations for the selected cytokinesis-related genes in the budding yeast; namely, Mcm1, Ndd1, and Fkh2, which form a transcription factor complex to control expression of the <jats:italic>CLB2<\/jats:italic> cluster (i.e. <jats:italic>BUD4<\/jats:italic>, <jats:italic>CHS2<\/jats:italic>, <jats:italic>IQG1<\/jats:italic>, and <jats:italic>CDC5<\/jats:italic>).<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>In this study, using <jats:italic>S. cerevisiae<\/jats:italic> as a model system, NCA was successfully applied to infer similar regulatory actions of transcription factor activities from two various microarray databases and several partial transcription factor-gene connectivity datasets for selected cytokinesis-related genes independent of data sizes. The regulated action for four selected cytokinesis-related genes (<jats:italic>BUD4<\/jats:italic>, <jats:italic>CHS2<\/jats:italic>, <jats:italic>IQG1<\/jats:italic>, and <jats:italic>CDC5<\/jats:italic>) belongs to the M-phase or M\/G1 phase, consistent with the empirical observations that in <jats:italic>S. cerevisiae<\/jats:italic>, the Mcm1-Ndd1-Fkh2 transcription factor complex can regulate expression of the cytokinesis-related genes <jats:italic>BUD4<\/jats:italic>, <jats:italic>CHS2<\/jats:italic>, <jats:italic>IQG1<\/jats:italic>, and <jats:italic>CDC5<\/jats:italic>. Since Bud4, Iqg1, and Cdc5 are highly conserved between human and yeast, results obtained from NCA for cytokinesis in the budding yeast can lead to a suggestion that human cells should have the transcription regulator(s) as the budding yeast Mcm1-Ndd1-Fkh2 transcription factor complex in controlling occurrence of cytokinesis.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1752-0509-3-110","type":"journal-article","created":{"date-parts":[[2009,12,1]],"date-time":"2009-12-01T11:24:13Z","timestamp":1259666653000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Inferring a transcriptional regulatory network of the cytokinesis-related genes by network component analysis"],"prefix":"10.1186","volume":"3","author":[{"given":"Shun-Fu","family":"Chen","sequence":"first","affiliation":[]},{"given":"Yue-Li","family":"Juang","sequence":"additional","affiliation":[]},{"given":"Wei-Kang","family":"Chou","sequence":"additional","affiliation":[]},{"given":"Jin-Mei","family":"Lai","sequence":"additional","affiliation":[]},{"given":"Chi-Ying F","family":"Huang","sequence":"additional","affiliation":[]},{"given":"Cheng-Yan","family":"Kao","sequence":"additional","affiliation":[]},{"given":"Feng-Sheng","family":"Wang","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2009,11,27]]},"reference":[{"issue":"5680","key":"378_CR1","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1126\/science.1097931","volume":"305","author":"AR Skop","year":"2004","unstructured":"Skop AR, Liu HB, Yates J, Meyer BJ, Heald R: Dissection of the mammalian midbody proteome reveals conserved cytokinesis mechanisms. 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