i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly.
i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly.
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DOI：
10.1093/nar/gkv395
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发表时间：
2015-07-01
影响因子：
14.9
通讯作者：
Aerts S
中科院分区：
文献类型：
--
作者：
Imrichová H;Hulselmans G;Atak ZK;Potier D;Aerts S
i-cisTarget是一个网络工具，用于预测一组基因组区域的调节子，例如ChIP-seq峰或共调节/类似增强子。i-cisTarget也可用于从一组共表达基因开始鉴定上游调节子及其靶增强子。虽然i-cisTarget的原始版本专注于果蝇数据，但2015年的更新也提供了对人类和小鼠数据的支持。i-cisTarget检测在输入区域集中富集的转录因子基序（位置权重矩阵）和实验数据轨道（例如来自ENCODE，Roadmap Epigenomics）。作为实验数据跟踪，我们包括转录因子ChIP-seq数据、组蛋白修饰ChIP-seq数据和开放染色质数据。基本的处理方法是基于一个排名和恢复程序，允许准确地确定丰富的异构数据集，同时也区分直接从间接的目标区域通过“前沿”分析。我们在各种尤文肉瘤数据集上展示了i-cisTarget，以从ChIP-seq，差异ATAC-seq，差异H3 K27 ac和差异基因表达数据开始识别EWS-FLI 1靶标。i-cisTarget的使用是免费的，对所有人开放，没有登录要求。网址：http://gbiomed.kuleuven.be/apps/lcb/i-cisTarget
i-cisTarget is a web tool to predict regulators of a set of genomic regions, such as ChIP-seq peaks or co-regulated/similar enhancers. i-cisTarget can also be used to identify upstream regulators and their target enhancers starting from a set of co-expressed genes. Whereas the original version of i-cisTarget was focused on Drosophila data, the 2015 update also provides support for human and mouse data. i-cisTarget detects transcription factor motifs (position weight matrices) and experimental data tracks (e.g. from ENCODE, Roadmap Epigenomics) that are enriched in the input set of regions. As experimental data tracks we include transcription factor ChIP-seq data, histone modification ChIP-seq data and open chromatin data. The underlying processing method is based on a ranking-and-recovery procedure, allowing accurate determination of enrichment across heterogeneous datasets, while also discriminating direct from indirect target regions through a ‘leading edge’ analysis. We illustrate i-cisTarget on various Ewing sarcoma datasets to identify EWS-FLI1 targets starting from ChIP-seq, differential ATAC-seq, differential H3K27ac and differential gene expression data. Use of i-cisTarget is free and open to all, and there is no login requirement. Address: http://gbiomed.kuleuven.be/apps/lcb/i-cisTarget.
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DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
5.8
作者：
Liberzon, Arthur;Subramanian, Aravind;Mesirov, Jill P.
通讯作者：
Mesirov, Jill P.
影响因子：
16
作者：
Heinz S;Benner C;Spann N;Bertolino E;Lin YC;Laslo P;Cheng JX;Murre C;Singh H;Glass CK
通讯作者：
Glass CK
影响因子：
14.9
作者：
Meyer LR;Zweig AS;Hinrichs AS;Karolchik D;Kuhn RM;Wong M;Sloan CA;Rosenbloom KR;Roe G;Rhead B;Raney BJ;Pohl A;Malladi VS;Li CH;Lee BT;Learned K;Kirkup V;Hsu F;Heitner S;Harte RA;Haeussler M;Guruvadoo L;Goldman M;Giardine BM;Fujita PA;Dreszer TR;Diekhans M;Cline MS;Clawson H;Barber GP;Haussler D;Kent WJ
通讯作者：
Kent WJ
影响因子：
5.8
作者：
Montgomery, SB;Griffith, OL;Jones, SJM
通讯作者：
Jones, SJM