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About CoNekT and diurnal.tools

CoNekT has been developed within the EvoRepro project and is supported primarily by ERA-CAPs and the Max Planck Society. The source code can be found on Github.

Diurnal.plant.tools is an online database addressing the challenges of studying diurnal gene expression in plants. It compiles data from 22 studies across the Archaeplastida kingdom and offers user-friendly tools for exploring gene expression profiles. The platform enables users to investigate specific genes or processes and facilitates advanced analyses, including cross-species comparisons and co-expression network exploration. With a focus on key biological questions, the database provides a valuable resource for researchers seeking insights into the evolution and conservation of diurnal gene expression in plants. The original paper publishing this database can be found at https://doi.org/10.1093/pcp/pcz176. An update in 2024 includes new data for five additional species.

Publications

Related publications

• Phylogenomic analysis of gene co-expression networks reveals evolution of functional modules, C. Ruprecht, S. Proost, M. Hernandez-Coronado, C. Ortiz-Ramirez, D. Lang, S. A. Rensing, J. D. Becker, K. Vandepoele, M. Mutwil, The Plant Journal (2017)
• Beyond genomics: studying evolution with gene networks, C. Ruprecht, N. Vaid, S. Proost, S. Persson, M. Mutwil, Trends in Plant Science (2017)
• PlaNet: Comparative Co-Expression Network Analyses for Plants, S. Proost, M.Mutwil, Plant Genomics Databases (Book Chapter) (2017)
• Tools of the trade: studying molecular networks in plants, S. Proost, M.Mutwil, Current Opinion in Plant Biology (2016)
• FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants, C. Ruprecht, A. Mendrinna, T. Tohge, A. Sampathkumar, S. Klie, A. R. Fernie, Z. Nikoloski, S. Persson, M. Mutwil, Plant Physiology (2016)
• Elucidating gene function and function evolution through comparison of co-expression networks of plants, B. O.Hansen, N.Vaid, M. Musialak-Lange, M. Janowski, M. Mutwil, Frontiers in Plant Science (2014)
• Towards revealing the functions of all genes in plants, S. Y. Rhee, M. Mutwil, Trends in Plant Science (2013)
• PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species. M. Mutwil, S. Klie, T. Tohge, F. M. Giorgi, O. Wilkins, M.M. Campbell, A.R. Fernie, B. Usadel, Z. Nikoloski, S. Persson, The Plant Cell (2011)
• Malaria.tools—comparative genomic and transcriptomic database for Plasmodium species, Qiao Wen Tan, Marek Mutwil, Nucleic Acids Research (2020) 
• Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses, Qiao Wen Tan, Peng Ken Lim, Zhong Chen, Asher Pasha, Nicholas Provart, Marius Arend, Zoran Nikoloski, Marek Mutwil, Nature communications (2023) 
• Fungi. guru: Comparative genomic and transcriptomic resource for the fungi kingdom, Jolyn Jia Jia Lim, Jace Koh, Jia Rong Moo, Erielle Marie Fajardo Villanueva, Dhira Anindya Putri, Yuen Shan Lim, Wei Song Seetoh, Sriya Mulupuri, Janice Wan Zhen Ng, Nhi Le Uyen Nguyen, Rinta Reji, Herman Foo, Margaret Xuan Zhao, Tong Ling Chan, Edbert Edric Rodrigues, Ryanjit Singh Kairon, Ker Min Hee, Natasha Cassandra Chee, Ann Don Low, Zoe Hui Xin Chen, Shan Chun Lim, Vanessa Lunardi, Tuck Choy Fong, Cherlyn Xin'Er Chua, Kenny Ting Sween Koh, Irene Julca, Riccardo Delli-Ponti, Jonathan Wei Xiong Ng, Marek Mutwil, Computational and Structural Biotechnology Journal (2020) 
• Protist.guru: A Comparative Transcriptomics Database for Protists, Erielle Marie Fajardo Villanueva, Peng Ken Lim, Jolyn Jia Jia Lim, Shan Chun Lim, Pei Yi Lau, Kenny Ting Sween Koh, Emmanuel Tan, Ryanjit Singh Kairon, Wei An See, Jian Xiang Liao, Ker Min Hee, Varsheni Vijay, Ishani Maitra, Chong Jun Boon, Kevin Fo, Yee Tat Wang, Ryan Jaya, Li Anne Hew, Yong Yee Lim, Wei Quan Lee, Zhi Qi Lee, Herman Foo, Adriana Lopes Dos Santos, Marek Mutwil, Journal of Molecular Biology (2022) 
• Bacteria.guru: comparative transcriptomics and co-expression database for bacterial pathogens, Peng Ken Lim, Emilia Emmanuelle Davey, Sean Wee, Wei Song Seetoh, Jong Ching Goh, Xinghai Zheng, Sean Kia Ann Phang, Eugene Sheng Kai Seah, Janice Wan Zhen Ng, Xavier Jia Hui Wee, Aloysius Jun Hui Quek, Jordan JingHeng Lim, Edbert Edric Rodrigues, Heesoo Lee, Chin Yong Lim, Wei Zhi Tan, Yuet Ruh Dan, Bronson Lee, Samuel En Le Chee, Zachary Ze En Lim, Jia Sheng Guan, Ivan Jia Le Tan, Trinidad Jeremiah Arong, Marek Mutwil, Journal of Molecular Biology (2022) 

Links

• http://www.gene2function.de : the first version of PlaNet

Other databases built using the CoNekT framework include:

• malaria.tools (Tan & Mutwil, 2020)
• conekt.plant.tools (Tan et al., 2023)
• fungi.guru (Lim et al., 2020)
• protist.guru (Villanueva et al., 2022)
• bacteria.guru (Lim et al., 2022)