• Genomics & Informatics
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• v.5 no.4
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• pp.143-151
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• 2007

To understand the mechanism of transcriptional regulation, it is essential to detect promoters and regulatory elements. Various kinds of methods have been introduced to improve the prediction accuracy of regulatory elements. Since there are few experimentally validated regulatory elements, previous studies have used criteria based solely on the level of scores over background sequences. However, selecting the detection criteria for different prediction methods is not feasible. Here, we studied the calibration of thresholds to improve regulatory element prediction. We predicted a regulatory element using MATCH, which is a powerful tool for transcription factor binding site (TFBS) detection. To increase the prediction accuracy, we used a regulatory potential (RP) score measuring the similarity of patterns in alignments to those in known regulatory regions. Next, we calibrated the thresholds to find relevant scores, increasing the true positives while decreasing possible false positives. By applying various thresholds, we compared predicted regulatory elements with validated regulatory elements from the Open Regulatory Annotation (ORegAnno) database. The predicted regulators by the selected threshold were validated through enrichment analysis of muscle-specific gene sets from the Tissue-Specific Transcripts and Genes (T-STAG) database. We found 14 known muscle-specific regulators with a less than a 5% false discovery rate (FDR) in a single TFBS analysis, as well as known transcription factor combinations in our combinatorial TFBS analysis.

• Korean Journal of Plant Taxonomy
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• v.51 no.1
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• pp.10-17
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• 2021

Invasive alien species management is pivotal for biodiversity conservation. Commelina caroliniana Walter, from the family Commelinaceae, is an alien plant native to the Himalayas and India, but it has been widely introduced around the world, including in the United States, Brazil, Philippines, and Japan. In Korea, the first population was found growing adjacent to agricultural land and farm roads on Jejudo Island, and field observations confirmed the presence of at least nine populations there. It is similar morphologically to C. diffusa Burm. f. but can be distinguished by involucral bracts that are ciliate at the base, hairs on the peduncle and obsolete upper cincinnus, brown spots on its 4-lobed antherode, and seed surfaces that are smooth to slightly alveolate. It was determined to have an invasiveness low score of 8 according to the Korean 'Invasive Alien Plant Risk Assessment', suggesting that it may spread to natural habitats. Although the current distribution of C. caroliniana is restricted to Jeju-si, it has spread dramatically in many other areas of the world. At present, it has had a limited impact on the local environment, but local and regulatory authorities should pay close attention to this plant and take measures to prevent its expansion in the future.