{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,24]],"date-time":"2024-08-24T12:13:09Z","timestamp":1724501589329},"reference-count":63,"publisher":"Oxford University Press (OUP)","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>An important topic in systems biology is the reverse engineering of regulatory mechanisms through reconstruction of context-dependent gene networks. A major challenge is to identify the genes and the regulations specific to a condition or phenotype, given that regulatory processes are highly connected such that a specific response is typically accompanied by numerous collateral effects. In this study, we design a multi-layer approach that is able to reconstruct condition-specific genes and their regulation through an integrative analysis of large-scale information of gene expression, protein interaction and transcriptional regulation (transcription factor-target gene relationships). We establish the accuracy of our methodology against synthetic datasets, as well as a yeast dataset. We then extend the framework to the application of higher eukaryotic systems, including human breast cancer and Arabidopsis thaliana cold acclimation. Our study identified TACSTD2 (TROP2) as a target gene for human breast cancer and discovered its regulation by transcription factors CREB, as well as NFkB. We also predict KIF2C is a target gene for ER\u2212\/HER2\u2212 breast cancer and is positively regulated by E2F1. The predictions were further confirmed through experimental studies.<\/jats:p>\n               <jats:p>Availability: The implementation and detailed protocol of the layer approach is available at http:\/\/www.egr.msu.edu\/changroup\/Protocols\/Three-layer%20approach%20to%20reconstruct%20condition.html.<\/jats:p>\n               <jats:p>Contact: \u00a0krischan@egr.msu.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt186","type":"journal-article","created":{"date-parts":[[2013,4,23]],"date-time":"2013-04-23T08:25:11Z","timestamp":1366705511000},"page":"1541-1552","source":"Crossref","is-referenced-by-count":11,"title":["A multi-layer inference approach to reconstruct condition-specific genes and their regulation"],"prefix":"10.1093","volume":"29","author":[{"given":"Ming","family":"Wu","sequence":"first","affiliation":[{"name":"1 Department of Computer Science and Engineering, 2Department of Microbiology and Molecular Genetics, 3Department of Chemical Engineering and Material Science and 4Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824,USA"}]},{"given":"Li","family":"Liu","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Engineering, 2Department of Microbiology and Molecular Genetics, 3Department of Chemical Engineering and Material Science and 4Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824,USA"}]},{"given":"Hussein","family":"Hijazi","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Engineering, 2Department of Microbiology and Molecular Genetics, 3Department of Chemical Engineering and Material Science and 4Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824,USA"}]},{"given":"Christina","family":"Chan","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Engineering, 2Department of Microbiology and Molecular Genetics, 3Department of Chemical Engineering and Material Science and 4Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824,USA"},{"name":"1 Department of Computer Science and Engineering, 2Department of Microbiology and Molecular Genetics, 3Department of Chemical Engineering and Material Science and 4Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824,USA"},{"name":"1 Department of Computer Science and Engineering, 2Department of Microbiology and Molecular Genetics, 3Department of Chemical Engineering and Material Science and 4Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824,USA"}]}],"member":"286","published-online":{"date-parts":[[2013,4,22]]},"reference":[{"key":"2023012810441582600_btt186-B1","first-page":"P4","article-title":"P4-09-11: kinesin family member 2C (KIF2C) is a new surrogate prognostic marker in breast cancer (BC)","volume":"71","author":"Abdel-Fatah","year":"2012","journal-title":"Cancer Res."},{"key":"2023012810441582600_btt186-B2","doi-asserted-by":"crossref","first-page":"37636","DOI":"10.1074\/jbc.M605895200","article-title":"A R2R3 type MYB transcription factor is involved in the cold regulation of CBF genes and in acquired freezing tolerance","volume":"281","author":"Agarwal","year":"2006","journal-title":"J. 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