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ConnecTF: A platform to integrate transcription factor-gene interactions and validate regulatory networks.
Brooks, MD, Juang, CL, Katari, MS, Alvarez, JM, Pasquino, A, Shih, HJ, Huang, J, Shanks, C, Cirrone, J, Coruzzi, GM
Plant physiology. 2021;(1):49-66
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Abstract
Deciphering gene regulatory networks (GRNs) is both a promise and challenge of systems biology. The promise lies in identifying key transcription factors (TFs) that enable an organism to react to changes in its environment. The challenge lies in validating GRNs that involve hundreds of TFs with hundreds of thousands of interactions with their genome-wide targets experimentally determined by high-throughput sequencing. To address this challenge, we developed ConnecTF, a species-independent, web-based platform that integrates genome-wide studies of TF-target binding, TF-target regulation, and other TF-centric omic datasets and uses these to build and refine validated or inferred GRNs. We demonstrate the functionality of ConnecTF by showing how integration within and across TF-target datasets uncovers biological insights. Case study 1 uses integration of TF-target gene regulation and binding datasets to uncover TF mode-of-action and identify potential TF partners for 14 TFs in abscisic acid signaling. Case study 2 demonstrates how genome-wide TF-target data and automated functions in ConnecTF are used in precision/recall analysis and pruning of an inferred GRN for nitrogen signaling. Case study 3 uses ConnecTF to chart a network path from NLP7, a master TF in nitrogen signaling, to direct secondary TF2s and to its indirect targets in a Network Walking approach. The public version of ConnecTF (https://ConnecTF.org) contains 3,738,278 TF-target interactions for 423 TFs in Arabidopsis, 839,210 TF-target interactions for 139 TFs in maize (Zea mays), and 293,094 TF-target interactions for 26 TFs in rice (Oryza sativa). The database and tools in ConnecTF will advance the exploration of GRNs in plant systems biology applications for model and crop species.
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[Research advance in cyclic hydroxamic acids, main allelochemicals of Zea mays].
Nie, C, Lou, S, Zeng, R, Wang, J, Huang, J, Li, M
Ying yong sheng tai xue bao = The journal of applied ecology. 2004;(6):1079-82
Abstract
The research advance in cyclic hydroxamic acids was reviewed in this paper. Cyclic hydroxamic acids are the important natural products of cereal crops. They and their respective derivatives are the constitutive compounds of a wide variety of gramineous plants and few dicot plants. They have structural diversity and different natural occurrences. Because of their phytotoxic properties, cyclic hydroxamic acids show a great variety of biological activities. They are the defensive agents against plant diseases, pests, nematodes and other plants. The distribution of cyclic hydroxamic acids in Zea mays and their variation in relation to the age were focused on in the paper. In Zea mays, there are structural diversity of cyclic hydroxamic acids and related benzoxazolinones. DIMBOA (1,4-benzoxazin-3(4H)-ones) is the most abundant derivative in Zea mays. The content of cyclic hydroxamic acids is strongly cultivar-dependent in Zea mays. Hydroxamic acids are not present in seeds. After germination, the level of DIMBOA increases, and the maximum level occurs in young seedlings a few days after germination. DIMBOA exists in all parts of plants, and its concentration is generally higher in shoots than in roots. In all stages, the young leaves of Zea mays have relatively high content of DIMBOA. The concentrations of these hydroxamic acids are highly dependent on environmental growth conditions. Under UV-light and water deficiencies, the levels of hydroxamic acids in plant increase rapidly. Cyclic hydroxamic acids exuded by Zea mays root can be quantitatively analyzed by HPLC. Supplying iron can significantly increase the exudation of DIMBOA from Zea mays root.