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Brooks MD, Juang CL, Katari MS, Alvarez JM, Pasquino A, Shih HJ, Huang J, Shanks C, Cirrone J, Coruzzi GM. ConnecTF: A platform to integrate transcription factor-gene interactions and validate regulatory networks. PLANT PHYSIOLOGY 2021; 185:49-66. [PMID: 33631799 PMCID: PMC8133578 DOI: 10.1093/plphys/kiaa012] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/27/2020] [Indexed: 05/08/2023]
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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Affiliation(s)
- Matthew D Brooks
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
- USDA ARS Global Change and Photosynthesis Research Unit, Urbana, IL, USA
| | - Che-Lun Juang
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
| | - Manpreet Singh Katari
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
| | - José M Alvarez
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Angelo Pasquino
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
| | - Hung-Jui Shih
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
| | - Ji Huang
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
| | - Carly Shanks
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
| | - Jacopo Cirrone
- Courant Institute for Mathematical Sciences, Department of Computer Science, New York University NY, USA
| | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
- Author for communication: (G.C.)
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