YTRP: a repository for yeast transcriptional regulatory pathways.
YTRP: a repository for yeast transcriptional regulatory pathways.
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DOI：
10.1093/database/bau014
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发表时间：
2014
期刊：
影响因子：
--
通讯作者：
Wu WS
中科院分区：
文献类型：
--
作者：
Yang TH;Wang CC;Wang YC;Wu WS
转录因子（TF）的调控靶标可以通过TF扰动实验来识别，该实验揭示了由于TF的扰动（缺失或过度表达）而导致的表达变化。但特定 TF 的确定目标包括直接和间接监管目标。研究表明，大多数TFPE识别的调控靶点都是间接的，这表明TF基因调控主要是通过由中间TF组成的转录调控途径（TRP）。如果不识别这些 TRP，就很难理解 TF 如何监管其间接目标。由于目前还没有这样的数据库存放酿酒酵母潜在的TRP，这促使我们构建YTRP（酵母转录调控途径）数据库。对于不同实验条件下的每个 TF-基因调控对，根据图论开发的 TRP 挖掘程序自动枚举了指定实验条件下两个底层网络（使用经过实验验证的 TF-基因结合对和文献中的 TF-基因调控对构建）中所有可能的 TRP。 TF 基因调控对的枚举 TRP 为 TF 及其调控靶点背后的分子机制提供了可通过实验检验的假设。 YTRP 可在线获取：http://cosbi3.ee.ncku.edu.tw/YTRP/。我们相信，存放在该数据库中的 TRP 将极大地提高 TFPE 数据的有用性，供酵母生物学家研究 TF 与其敲除靶标之间的调控机制。数据库网址：http://cosbi3.ee.ncku.edu.tw/YTRP/
Regulatory targets of transcription factors (TFs) can be identified by the TF perturbation experiments, which reveal the expression changes owing to the perturbation (deletion or overexpression) of TFs. But the identified targets of a given TF consist of both direct and indirect regulatory targets. It has been shown that most of the TFPE-identified regulatory targets are indirect, indicating that TF-gene regulation is mainly through transcriptional regulatory pathways (TRPs) consisting of intermediate TFs. Without identification of these TRPs, it is not easy to understand how a TF regulates its indirect targets. Because there is no such database depositing the potential TRPs for Saccharomyces cerevisiae now, this motivates us to construct the YTRP (Yeast Transcriptional Regulatory Pathway) database. For each TF-gene regulatory pair under different experimental conditions, all possible TRPs in two underlying networks (constructed using experimentally verified TF-gene binding pairs and TF-gene regulatory pairs from the literature) for the specified experimental conditions were automatically enumerated by TRP mining procedures developed from the graph theory. The enumerated TRPs of a TF-gene regulatory pair provide experimentally testable hypotheses for the molecular mechanisms behind a TF and its regulatory target. YTRP is available online at http://cosbi3.ee.ncku.edu.tw/YTRP/. We believe that the TRPs deposited in this database will greatly improve the usefulness of TFPE data for yeast biologists to study the regulatory mechanisms between a TF and its knocked-out targets. Database URL: http://cosbi3.ee.ncku.edu.tw/YTRP/
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影响因子：
30.8
作者：
Yeger-Lotem, Esti;Riva, Laura;Su, Linhui Julie;Gitler, Aaron D.;Cashikar, Anil G.;King, Oliver D.;Auluck, Pavan K.;Geddie, Melissa L.;Valastyan, Julie S.;Karger, David R.;Lindquist, Susan;Fraenkel, Ernest
通讯作者：
Fraenkel, Ernest
DOI：
10.1073/pnas.0508647102
发表时间：
2005-11-29
影响因子：
11.1
作者：
Hwang, D;Rust, AG;Bolouri, H
通讯作者：
Bolouri, H
影响因子：
7.3
作者：
Huang SS;Fraenkel E
通讯作者：
Fraenkel E
影响因子：
9.9
作者：
Suthram, Silpa;Beyer, Andreas;Karp, Richard M.;Eldar, Yonina;Ideker, Trey
通讯作者：
Ideker, Trey
影响因子：
14.9
作者：
Abdulrehman D;Monteiro PT;Teixeira MC;Mira NP;Lourenço AB;dos Santos SC;Cabrito TR;Francisco AP;Madeira SC;Aires RS;Oliveira AL;Sá-Correia I;Freitas AT
通讯作者：
Freitas AT