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In this paper, the regulatory mechanism of mouse neural stem cell (NSC) differentiation by <jats:italic>tmem59<\/jats:italic> is explored on the genome-level.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We identified regulators of <jats:italic>tmem59<\/jats:italic> during the differentiation of mouse NSCs from a compendium of expression profiles. Based on the microarray experiment, we developed the parallelized SWNI algorithm to reconstruct gene regulatory networks of mouse neural stem cells. From the inferred <jats:italic>tmem59<\/jats:italic> related gene network including 36 genes, <jats:italic>pou6f1<\/jats:italic> was identified to regulate <jats:italic>tmem59<\/jats:italic> significantly and might play an important role in the differentiation of NSCs in mouse brain. There are four pathways shown in the gene network, indicating that <jats:italic>tmem59<\/jats:italic> locates in the downstream of the signalling pathway. The real-time RT-PCR results shown that the over-expression of <jats:italic>pou6f1<\/jats:italic> could significantly up-regulate <jats:italic>tmem59<\/jats:italic> expression in C17.2 NSC line. 16 out of 36 predicted genes in our constructed network have been reported to be AD-related, including <jats:italic>Ace<\/jats:italic>, <jats:italic>aqp1<\/jats:italic>, <jats:italic>arrdc3<\/jats:italic>, <jats:italic>cd14<\/jats:italic>, <jats:italic>cd59a<\/jats:italic>, <jats:italic>cds1<\/jats:italic>, <jats:italic>cldn1<\/jats:italic>, <jats:italic>cox8b<\/jats:italic>, <jats:italic>defb11<\/jats:italic>, <jats:italic>folr1<\/jats:italic>, <jats:italic>gdi2<\/jats:italic>, <jats:italic>mmp3<\/jats:italic>, <jats:italic>mgp<\/jats:italic>, <jats:italic>myrip<\/jats:italic>, <jats:italic>Ripk4<\/jats:italic>, <jats:italic>rnd3<\/jats:italic>, and <jats:italic>sncg<\/jats:italic>. The localization of <jats:italic>tmem59<\/jats:italic> related genes and functional-related gene groups based on the Gene Ontology (GO) annotation was also identified.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Our findings suggest that the expression of <jats:italic>tmem59<\/jats:italic> is an important factor contributing to AD. The parallelized SWNI algorithm increased the efficiency of network reconstruction significantly. This study enables us to highlight novel genes that may be involved in NSC differentiation and provides a shortcut to identifying genes for AD.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1752-0509-5-152","type":"journal-article","created":{"date-parts":[[2011,9,29]],"date-time":"2011-09-29T06:19:35Z","timestamp":1317277175000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":29,"title":["Identifying Tmem59 related gene regulatory network of mouse neural stem cell from a compendium of expression profiles"],"prefix":"10.1186","volume":"5","author":[{"given":"Luwen","family":"Zhang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiangchun","family":"Ju","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yumin","family":"Cheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiuyun","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tieqiao","family":"Wen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2011,9,29]]},"reference":[{"key":"755_CR1","volume-title":"Bioinformatics and Functional Genomics","author":"P Jonathan","year":"2009","unstructured":"Jonathan P: Bioinformatics and Functional Genomics. 2009, Wiley-Blackwell Press"},{"key":"755_CR2","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1196\/annals.1407.019","volume":"1115","author":"AA Margolin","year":"2007","unstructured":"Margolin AA, Califano A: Theory and limitations of genetic network inference from microarray data. 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