{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,29]],"date-time":"2025-12-29T18:46:59Z","timestamp":1767034019952},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"24","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: MicroRNAs (miRNAs) are small non-coding RNAs that cause mRNA degradation and translational inhibition. They are important regulators of development and cellular homeostasis through their control of diverse processes. Recently, great efforts have been made to elucidate their regulatory mechanism, but the functions of most miRNAs and their precise regulatory mechanisms remain elusive. With more and more matched expression profiles of miRNAs and mRNAs having been made available, it is of great interest to utilize both expression profiles to discover the functional regulatory networks of miRNAs and their target mRNAs for potential biological processes that they may participate in.<\/jats:p><jats:p>Results: We present a probabilistic graphical model to discover functional miRNA regulatory modules at potential biological levels by integrating heterogeneous datasets, including expression profiles of miRNAs and mRNAs, with or without the prior target binding information. We applied this model to a mouse mammary dataset. It effectively captured several biological process specific modules involving miRNAs and their target mRNAs. Furthermore, without using prior target binding information, the identified miRNAs and mRNAs in each module show a large proportion of overlap with predicted miRNA target relationships, suggesting that expression profiles are crucial for both target identification and discovery of regulatory modules.<\/jats:p><jats:p>Contact: \u00a0bing.liu@unisa.edu.au; jiuyong.li@unisa.edu.au<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq576","type":"journal-article","created":{"date-parts":[[2010,12,1]],"date-time":"2010-12-01T08:08:45Z","timestamp":1291190925000},"page":"3105-3111","source":"Crossref","is-referenced-by-count":78,"title":["Identifying functional miRNA\u2013mRNA regulatory modules with correspondence latent dirichlet allocation"],"prefix":"10.1093","volume":"26","author":[{"given":"Bing","family":"Liu","sequence":"first","affiliation":[{"name":"1 School of Computer and Information Science, University of South Australia, Mawson Lakes, SA 5095, 2Centre for Cancer Biology, SA Pathology, Adelaide, SA 5000, 3School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA 5005, 4Department of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia, 5Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD 20892 and 6Laboratory of Molecular Technology, NCI-FCRDC, Frederick, MD 21702, USA"},{"name":"1 School of Computer and Information Science, University of South Australia, Mawson Lakes, SA 5095, 2Centre for Cancer Biology, SA Pathology, Adelaide, SA 5000, 3School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA 5005, 4Department of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia, 5Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD 20892 and 6Laboratory of Molecular Technology, NCI-FCRDC, Frederick, MD 21702, USA"}]},{"given":"Lin","family":"Liu","sequence":"additional","affiliation":[{"name":"1 School of Computer and Information Science, University of South Australia, Mawson Lakes, SA 5095, 2Centre for Cancer Biology, SA Pathology, Adelaide, SA 5000, 3School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA 5005, 4Department of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia, 5Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD 20892 and 6Laboratory of Molecular Technology, NCI-FCRDC, Frederick, MD 21702, USA"}]},{"given":"Anna","family":"Tsykin","sequence":"additional","affiliation":[{"name":"1 School of Computer and Information Science, University of South Australia, Mawson Lakes, SA 5095, 2Centre for Cancer Biology, SA Pathology, Adelaide, SA 5000, 3School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA 5005, 4Department of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia, 5Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD 20892 and 6Laboratory of Molecular Technology, NCI-FCRDC, Frederick, MD 21702, USA"},{"name":"1 School of Computer and Information Science, University of South Australia, Mawson Lakes, SA 5095, 2Centre for Cancer Biology, SA Pathology, Adelaide, SA 5000, 3School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA 5005, 4Department of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia, 5Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD 20892 and 6Laboratory of Molecular Technology, NCI-FCRDC, Frederick, MD 21702, USA"}]},{"given":"Gregory J.","family":"Goodall","sequence":"additional","affiliation":[{"name":"1 School of Computer and Information Science, University of South Australia, Mawson Lakes, SA 5095, 2Centre for Cancer Biology, SA Pathology, Adelaide, SA 5000, 3School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA 5005, 4Department of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia, 5Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD 20892 and 6Laboratory of Molecular Technology, NCI-FCRDC, Frederick, MD 21702, USA"},{"name":"1 School of Computer and Information Science, University of South Australia, Mawson Lakes, SA 5095, 2Centre for Cancer Biology, SA Pathology, Adelaide, SA 5000, 3School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA 5005, 4Department of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia, 5Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD 20892 and 6Laboratory of Molecular Technology, NCI-FCRDC, Frederick, MD 21702, USA"}]},{"given":"Jeffrey E.","family":"Green","sequence":"additional","affiliation":[{"name":"1 School of Computer and Information Science, University of South Australia, Mawson Lakes, SA 5095, 2Centre for Cancer Biology, SA Pathology, Adelaide, SA 5000, 3School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA 5005, 4Department of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia, 5Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD 20892 and 6Laboratory of Molecular Technology, NCI-FCRDC, Frederick, MD 21702, USA"}]},{"given":"Min","family":"Zhu","sequence":"additional","affiliation":[{"name":"1 School of Computer and Information Science, University of South Australia, Mawson Lakes, SA 5095, 2Centre for Cancer Biology, SA Pathology, Adelaide, SA 5000, 3School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA 5005, 4Department of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia, 5Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD 20892 and 6Laboratory of Molecular Technology, NCI-FCRDC, Frederick, MD 21702, USA"}]},{"given":"Chang Hee","family":"Kim","sequence":"additional","affiliation":[{"name":"1 School of Computer and Information Science, University of South Australia, Mawson Lakes, SA 5095, 2Centre for Cancer Biology, SA Pathology, Adelaide, SA 5000, 3School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA 5005, 4Department of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia, 5Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD 20892 and 6Laboratory of Molecular Technology, NCI-FCRDC, Frederick, MD 21702, USA"}]},{"given":"Jiuyong","family":"Li","sequence":"additional","affiliation":[{"name":"1 School of Computer and Information Science, University of South Australia, Mawson Lakes, SA 5095, 2Centre for Cancer Biology, SA Pathology, Adelaide, SA 5000, 3School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA 5005, 4Department of Medicine, The University of Adelaide, Adelaide, SA 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