TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data.
TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data.
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TIMEOR：一个基于网络的工具，从多组学数据中发现时间调节机制。
DOI：
10.1093/nar/gkab384
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发表时间：
2021-07-02
影响因子：
14.9
通讯作者：
Larschan E
中科院分区：
文献类型：
--
作者：
Conard AM;Goodman N;Hu Y;Perrimon N;Singh R;Lawrence C;Larschan E
Uncovering how transcription factors regulate their targets at DNA, RNA and protein levels over time is critical to define gene regulatory networks (GRNs) and assign mechanisms in normal and diseased states. RNA-seq is a standard method measuring gene regulation using an established set of analysis stages. However, none of the currently available pipeline methods for interpreting ordered genomic data (in time or space) use time-series models to assign cause and effect relationships within GRNs, are adaptive to diverse experimental designs, or enable user interpretation through a web-based platform. Furthermore, methods integrating ordered RNA-seq data with protein–DNA binding data to distinguish direct from indirect interactions are urgently needed. We present TIMEOR (Trajectory Inference and Mechanism Exploration with Omics data in R), the first web-based and adaptive time-series multi-omics pipeline method which infers the relationship between gene regulatory events across time. TIMEOR addresses the critical need for methods to determine causal regulatory mechanism networks by leveraging time-series RNA-seq, motif analysis, protein–DNA binding data, and protein-protein interaction networks. TIMEOR’s user-catered approach helps non-coders generate new hypotheses and validate known mechanisms. We used TIMEOR to identify a novel link between insulin stimulation and the circadian rhythm cycle. TIMEOR is available at https://github.com/ashleymaeconard/TIMEOR.git and http://timeor.brown.edu. TIMEOR: novel web tool generates gene regulatory network and beyond to assign mechanism combining temporal and multi-omics data.
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影响因子：
7.7
作者：
Florez, Jose C.
通讯作者：
Florez, Jose C.
DOI：
10.1152/ajpendo.1996.271.2.e246
发表时间：
1996-08-01
影响因子：
5.1
作者：
Boden, G;Ruiz, J;Chen, XH
通讯作者：
Chen, XH
影响因子：
14.9
作者：
Franceschini A;Szklarczyk D;Frankild S;Kuhn M;Simonovic M;Roth A;Lin J;Minguez P;Bork P;von Mering C;Jensen LJ
通讯作者：
Jensen LJ
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：
11.4
作者：
Brent, Michael R.
通讯作者：
Brent, Michael R.