Integrating regulatory motif discovery and genome-wide expression analysis.

Conlon EM; Liu XS; Lieb JD; Liu JS

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Integrating regulatory motif discovery and genome-wide expression analysis.

机译：整合调节基序发现和全基因组表达分析。

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摘要

We propose motif regressor for discovering sequence motifs upstream of genes that undergo expression changes in a given condition. The method combines the advantages of matrix-based motif finding and oligomer motif-expression regression analysis, resulting in high sensitivity and specificity. motif regressor is particularly effective in discovering expression-mediating motifs of medium to long width with multiple degenerate positions. When applied to Saccharomyces cerevisiae, motif regressor identified the ROX1 and YAP1 motifs from Rox1p and Yap1p overexpression experiments, respectively; predicted that Gcn4p may have increased activity in YAP1 deletion mutants; reported a group of motifs (including GCN4, PHO4, MET4, STRE, USR1, RAP1, M3A, and M3B) that may mediate the transcriptional response to amino acid starvation; and found all of the known cell-cycle regulation motifs from 18 expression microarrays over two cell cycles.

机译：我们提出了基序回归因子，用于发现在给定条件下经历表达变化的基因上游的序列基序。该方法结合了基于矩阵的基序发现和低聚物基序表达回归分析的优势，从而具有很高的灵敏度和特异性。主题回归器在发现具有多个简并位置的中等至长宽度的介导表达的主题中特别有效。当应用于酿酒酵母时，基序回归因子分别从Rox1p和Yap1p过表达实验中鉴定出ROX1和YAP1基序。预测Gcn4p可能在YAP1缺失突变体中具有增加的活性；报告了一组可能介导对氨基酸饥饿的转录反应的基序（包括GCN4，PHO4，MET4，STRE，USR1，RAP1，M3A和M3B）；并在两个细胞周期中从18个表达微阵列中发现了所有已知的细胞周期调控基序。

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《Proceedings of the National Academy of Sciences of the United States of America》 |2003年第6期|P.3339-3344|共6页
作者
Conlon EM; Liu XS; Lieb JD; Liu JS;
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作者单位

Department of Statistics, Harvard University, 1 Oxford Street, Cambridge, MA 02138, USA.;

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收录信息美国《科学引文索引》(SCI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
原文格式 PDF
正文语种 eng
中图分类自然科学总论;
关键词
regulatory; Genome; Analysis of substances; overexpress; Width; 基因组;

机译：regulatory;Genome;Analysis of substances;overexpress;Width;基因组;

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1. Integrating Peak Colocalization and Motif Enrichment Analysis for the Discovery of Genome-Wide Regulatory Modules and Transcription Factor Recruitment Rules [J] . Mirko Ronzio, Federico Zambelli, Diletta Dolfini, Frontiers in Genetics . 2020,第1期

机译：集成峰上分层化和基序浓缩分析，以发现基因组监管模块和转录因子招聘规则
2. Genome-wide analysis of cis-regulatory element structure and discovery of motif-driven gene co-expression networks in grapevine [J] . Darren Chern Jan Wong, Rodrigo Lopez Gutierrez, Gregory Alan Gambetta, DNA research: an international journal for rapid publication of reports on genes and genomes . 2017,第3期

机译：全基因组的顺式调控元件结构分析和基元驱动的葡萄基因共表达网络的发现
3. Genome-wide analysis of cis-regulatory element structure and discovery of motif-driven gene co-expression networks in grapevine [J] . Wong Darren Chern Jan, Gutierrez Rodrigo Lopez, Gambetta Gregory Alan, DNA research: an international journal for rapid publication of reports on genes and genomes . 2017,第3期

机译：CIS-COMMINATION元素结构的基因组分析与葡萄葡萄葡萄球菌基因CO表达网络的发现
4. A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks [C] . Zhen Gao, Ruizhe Zhao, Jianhua Ruan Asia-Pacific Bioinformatics Conference . 2013

机译：一种基于启动子序列和基因共表达网络的基因组CIS调节元素发现方法
5. Genome-wide discovery of cis-regulatory RNA motifs and transcriptional regulatory networks. [D] . Xu, Xing. 2008

机译：全基因组范围内的顺式调控RNA基序和转录调控网络的发现。
6. Integrating regulatory motif discovery and genome-wide expression analysis [O] . Erin M. Conlon, X. Shirley Liu, Jason D. Lieb, 2003

机译：整合调节基序发现和全基因组表达分析
7. Integrating regulatory motif discovery and genome-wide expression analysis [O] . Conlon, Erin M., Liu, X. Shirley, Lieb, Jason D., 2003

机译：整合调节基序发现和全基因组表达分析

Integrating regulatory motif discovery and genome-wide expression analysis.

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