ConnecTF: A platform to integrate transcription factor–gene interactions and validate regulatory networks
| Autor: | Hung Jui Shih, Matthew D. Brooks, José M. Alvarez, Manpreet S. Katari, Jacopo Cirrone, Carly Shanks, Angelo Pasquino, Ji Huang, Che Lun Juang, Gloria M. Coruzzi |
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| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
0106 biological sciences
Crops Agricultural Physiology Computer science Systems biology Gene regulatory network Arabidopsis Plant Science Computational biology Genes Plant 01 natural sciences Zea mays 03 medical and health sciences Gene Expression Regulation Plant Genetics Gene Regulatory Networks Pruning (decision trees) Plant system Transcription factor 030304 developmental biology Regulation of gene expression 0303 health sciences biology Oryza biology.organism_classification Databases as Topic Breakthrough Technologies Tools and Resources Transcription Factor Gene 010606 plant biology & botany Transcription Factors |
| Zdroj: | Plant Physiol |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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