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| 1 | Integration of Known Transcription Factor Binding Site Information and Gene Expression Data to Advance from Co-Expression to Co-Regulation显示文摘The common approach to find co-regulated genes is to cluster genes based on gene expression. However, due to the limited information present in any dataset, genes in the same cluster might be co-expressed but not necessarily co-regulated. In this paper, we propose to integrate known transcription factor binding site information and gene expression data into a single clustering scheme. This scheme will find clusters of co-regulated genes that are not only expressed similarly under the measured conditions, but also share a regulatory structure that may explain their common regulation. We demonstrate the utility of this approach on a microarray dataset of yeast grown under different nutrient and oxygen limitations. Our integrated clustering method not only unravels many regulatory modules that are consistent with current biological knowledge, but also provides a more profound understanding of the underlying process. The added value of our approach, compared with the clustering solely based on gene expression, is its ability to uncover clusters of genes that are involved in more specific biological processes and are evidently regulated by a set of transcription factors. | Maarten Clements Eugene P. van Someren Theo A. Knijnenburg Marcel J.T. Reinders | 2007 | Genomics, Proteomics & Bioinformatics2007，5，2： | 4 |
| 2 | Daily nighttime melatonin reduces blood pressure in male patients with essential hypertension显示文摘 | Scheer FA Van Montfrans GA Van Someren E J | 2004 | J Hypertens2004，43，2： | 1 |
| 3 | An investigation into the benefits of resiting feeding tubes显示文摘 | Van Someren V Linnett SJ Stothers JK | 1984 | Pediatrics1984，74，： | 1 |
| 4 | Daily nighttime melatonin reduces blood pressure in male patients with essential hypertension 显示文摘 | Scheer FA Van Montgrans GA van Someren EJ | 2004 | Hypertension2004，，43： | 1 |
| 5 | More than a marker: interaction between the circadian regulation of temperature and sleep, age-related changes, and treatment possibilities 显示文摘 | Van Someren EJ | 2000 | Chronohiol Int2000，17，3： | 1 |
| 6 | The prevention and treatment of exercise-induced muscle damage 显示文摘 | Howatson G van Someren K A | 2008 | Sports Med2008，38，6： | 1 |
| 7 | Beneficial effect of transcranial magnetic stimulation on sleep in Parkinson's disease显示文摘 | van Dijk KD Most EI Van Someren EJ | 2009 | Mov Disord2009，24，6： | 1 |
| 8 | Effects of low-frequency cranial electrostimulation on the rest-activity rhythm and salivary cortisol in Alzheimer's disease显示文摘 | Scherder E Knol D van Someren E | 2003 | Neu-rorehabilitation and Neural Repair2003，17，2： | 1 |
| 9 | Genetic network modeling显示文摘 | Someren E P v Wessels L F A Backer E | 2002 | Pharmacogenomics2002，3，4： | 1 |
| 10 | Clinical update: melatonin and sleep disorders 显示文摘 | Arendt J Van Someren EJ Appleton R | 2008 | Cli Med2008，8，4： | 1 |
| 11 | Circadian and sleep disturbances in the elderly显示文摘 | Van Someren EJ | 2000 | Exp Gerontol2000，35，910： | 1 |
| 12 | A modified TRIMP to quantify the in-season training load of team sport players显示文摘 | Karl M.Stagno Rhys Thatcher Ken A.Van Someren | | 0，，06： | 1 |
| 13 | Peripheral electrical nerve stimulation and rest-activity rhythm in Alzheimer's disease显示文摘 | Luijpen MW Van Someren EJ | 2006 | J Sleep Res2006，15，4： | 1 |
| 14 | Thermoregulation and aging显示文摘 | Van Someren | 2007 | AmericanJournar of Physiology-Regulatory Integrative and Comparative Physiology2007，292，1： | 1 |
| 15 | Cir- eadian rhythmrrlated behavioral disturbances and struc- tural hypothalamic change in Alzheimer's disease显示文摘 | Hoogendijk WJ van Someren EJ Mirmiran M | 2006 | Int Psychogeniatr2006，8，3： | 1 |
| 16 | Reduction of scale invariance of activity fluctuations with aging and Alzheimer's disease:Involvement of the circadian pacemaker显示文摘 | Hu K Van Someren E J Shea SA | 2009 | Proc Natl Acad Sci U S A2009，106，： | 1 |
| 17 | Com- parison of physiological responses to open water kayak- ing and kayak ergometry显示文摘 | Someren K A Phillips G R W Palmer G S | 2000 | Int J Sports Med2000，21，： | 1 |
| 18 | Colocalization of corticotropin-releasing hormone and oestrogen receptor-alpha in the paraventricular nucleus of the hypothalamus in mood disorders 显示文摘 | Bao AM Hestiantoro A Van Someren EJ | 2005 | Brain2005，128，6： | 1 |
| 19 | A redundancybased method for the extraction of relation instances from the Web显示文摘 | de BOER V van SOMEREN M WIELINGA B J | 2007 | International Journal of Human-Computer Studies2007，65，9： | 1 |
| 20 | Daily night-time melatonin reduces blood pressure in male patients with essential hypertension显示文摘 | Scheer FA Van Monffrans GA van Someren EJ | 2004 | Hypertension2004，43，2： | 1 |
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