MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis.
MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis.
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Motiflab：用于图案发现和调节序列分析的工具和数据集成工作台。
DOI：
10.1186/1471-2105-14-9
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发表时间：
2013-01-16
影响因子：
3
通讯作者：
Drabløs F
中科院分区：
文献类型：
--
作者：
Klepper K;Drabløs F
传统的计算模体发现方法往往受到性能不佳。特别地，搜索与已知结合基序匹配的序列的方法倾向于预测许多非功能性结合位点，因为它们未能考虑细胞的生物学状态。近年来，全基因组研究产生了大量数据，这些数据有可能提高我们识别功能基序和结合位点的能力，例如关于不同细胞类型中染色质可及性和表观遗传状态的信息。然而，结合现有的基序发现工具使用这些数据并不总是微不足道的，特别是对于不熟悉生物信息学编程的研究人员。在这里，我们提出了MotifLab，一个通用的工作台，用于分析调控序列区域，发现转录因子结合位点和顺式调控模块。MotifLab支持全面的基序发现和分析，允许用户集成几种流行的基序发现工具以及不同类型的附加信息，包括系统发育保护，表观遗传标记，DNase超敏位点，ChIP-Seq数据，转录因子的位置结合偏好，转录因子相互作用和基因表达。MotifLab提供了几种数据处理操作，可用于创建，操作和分析数据对象，完整的分析工作流程可以在MotifLab中构建和自动执行，包括结果的图形表示。我们开发了MotifLab作为一个灵活的工作台，用于基因组背景下的基序分析。这个工作台的灵活性和有效性已被证明在选定的测试案例，特别是两个以前发表的基准数据集的单个图案和模块，和一个现实的例子，基因治疗与毛喉素。MotifLab可在http://www.motiflab.org免费获得。
Traditional methods for computational motif discovery often suffer from poor performance. In particular, methods that search for sequence matches to known binding motifs tend to predict many non-functional binding sites because they fail to take into consideration the biological state of the cell. In recent years, genome-wide studies have generated a lot of data that has the potential to improve our ability to identify functional motifs and binding sites, such as information about chromatin accessibility and epigenetic states in different cell types. However, it is not always trivial to make use of this data in combination with existing motif discovery tools, especially for researchers who are not skilled in bioinformatics programming. Here we present MotifLab, a general workbench for analysing regulatory sequence regions and discovering transcription factor binding sites and cis-regulatory modules. MotifLab supports comprehensive motif discovery and analysis by allowing users to integrate several popular motif discovery tools as well as different kinds of additional information, including phylogenetic conservation, epigenetic marks, DNase hypersensitive sites, ChIP-Seq data, positional binding preferences of transcription factors, transcription factor interactions and gene expression. MotifLab offers several data-processing operations that can be used to create, manipulate and analyse data objects, and complete analysis workflows can be constructed and automatically executed within MotifLab, including graphical presentation of the results. We have developed MotifLab as a flexible workbench for motif analysis in a genomic context. The flexibility and effectiveness of this workbench has been demonstrated on selected test cases, in particular two previously published benchmark data sets for single motifs and modules, and a realistic example of genes responding to treatment with forskolin. MotifLab is freely available at http://www.motiflab.org.
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影响因子：
3
作者：
Bailey TL;Bodén M;Whitington T;Machanick P
通讯作者：
Machanick P
DOI：
10.1093/bioinformatics/btr064
发表时间：
2011-04-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Grant CE;Bailey TL;Noble WS
通讯作者：
Noble WS
影响因子：
14.9
作者：
Dreszer TR;Karolchik D;Zweig AS;Hinrichs AS;Raney BJ;Kuhn RM;Meyer LR;Wong M;Sloan CA;Rosenbloom KR;Roe G;Rhead B;Pohl A;Malladi VS;Li CH;Learned K;Kirkup V;Hsu F;Harte RA;Guruvadoo L;Goldman M;Giardine BM;Fujita PA;Diekhans M;Cline MS;Clawson H;Barber GP;Haussler D;James Kent W
通讯作者：
James Kent W
TransFac及其模块移植：真核生物中的转录基因调节。
影响因子：
14.9
作者：
Matys V;Kel-Margoulis OV;Fricke E;Liebich I;Land S;Barre-Dirrie A;Reuter I;Chekmenev D;Krull M;Hornischer K;Voss N;Stegmaier P;Lewicki-Potapov B;Saxel H;Kel AE;Wingender E
通讯作者：
Wingender E
影响因子：
3
作者：
通讯作者：
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