Drosophila DNase I footprint database:: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster
Drosophila DNase I footprint database:: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster
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DOI：
10.1093/bioinformatics/bti173
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发表时间：
2005-04-15
期刊：
影响因子：
5.8
通讯作者：
Celniker, SE
中科院分区：
文献类型：
--
作者：
Bergman, CM;Carlson, JW;Celniker, SE
尽管开发出越来越多的计算工具来预测顺式调控序列，但转录因子结合位点的高质量数据集的可用性限制了基因调控生物信息学的进展。在此，我们基于对果蝇（黑腹果蝇）DNase I足迹的系统文献整理和基因组注释，呈现了这样一个数据集。利用201篇主要参考文献的实验结果，我们在黑腹果蝇基因组序列中对来自87个转录因子和101个靶基因的1367个结合位点进行了注释。这些数据将为果蝇转录调控的未来生物信息学分析提供丰富的资源，例如构建基序模型、训练顺式调控模块检测器、对比对工具进行基准测试以及对有关这一重要模式生物转录调控的大量文献继续进行文本挖掘。
Despite increasing numbers of computational tools developed to predict cis-regulatory sequences, the availability of high-quality datasets of transcription factor binding sites limits advances in the bioinformatics of gene regulation. Here we present such a dataset based on a systematic literature curation and genome annotation of DNase I footprints for the fruitfly, Drosophila melanogaster. Using the experimental results of 201 primary references, we annotated 1367 binding sites from 87 transcription factors and 101 target genes in the D.melanogaster genome sequence. These data will provide a rich resource for future bioinformatics analyses of transcriptional regulation in Drosophila such as constructing motif models, training cis-regulatory module detectors, benchmarking alignment tools and continued text mining of the extensive literature on transcriptional regulation in this important model organism.