About CKN
The Arabidopsis Comprehensive Knowledge Network (CKN) is a large-scale condition-agnostic assembly of current knowledge, offering broader insights into not only stress signalling, but also any other plant process. CKN is a network of experimentally observed physical interactions between molecular entities, encompassing protein-DNA interactions, interactions of smallRNA with transcripts, post-translational modifications, and protein-protein interactions in Arabidopsis.
The current version of CKN is v2.
A ranking system for the interaction reliability (see table below), allows researchers to evaluate how biologically credible and relevant individual interactions are.
CKN sources
The sources of CKN are as follows:| CKN-version | Interaction type | Ranks | DOI | Reference |
|---|---|---|---|---|
| v1 | binding | 1 | 10.1016/j.coviro.2012.09.004 | Elena, S. F., & Rodrigo, G. (2012). Towards an integrated molecular model of plant-virus interactions. Current Opinion in Virology, 2(6), 719–724. |
| v2 | transcription factor regulation | 2 | 10.1016/j.cub.2016.12.016 | Shani, E., Salehin, M., Zhang, Y., Sanchez, S. E., Doherty, C., Wang, R., … Estelle, M. (2017). Plant Stress Tolerance Requires Auxin-Sensitive Aux/IAA Transcriptional Repressors. Current Biology, 27(3), 437–444. |
| v2 | binding | 1, 2 | 10.1038/nature25184 | Smakowska-Luzan, E., Mott, G. A., Parys, K., Stegmann, M., Howton, T. C., Layeghifard, M., … Belkhadir, Y. (2018). An extracellular network of Arabidopsis leucine-rich repeat receptor kinases. Nature, 553(7688), 342–346. |
| v2 | transcription factor regulation | 2 | 10.1038/s41467-018-03921-6 | Xie, M., Chen, H., Huang, L., O’Neil, R. C., Shokhirev, M. N., & Ecker, J. R. (2018). A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development. Nature Communications, 9(1), 1–13. |
| v2 | post-translational modification | 2 | 10.1038/s41477-019-0378-z | Van Leene, J., Han, C., Gadeyne, A., Eeckhout, D., Matthijs, C., Cannoot, B., … De Jaeger, G. (2019). Capturing the phosphorylation and protein interaction landscape of the plant TOR kinase. Nature Plants, 5(3), 316–327. |
| v2 | binding | 2 | 10.1073/pnas.1603229113 | Yazaki, J., Galli, M., Kim, A. Y., Nito, K., Aleman, F., Chang, K. N., … Ecker, J. R. (2016). Mapping transcription factor interactome networks using HaloTag protein arrays. Proceedings of the National Academy of Sciences of the United States of America, 113(29), E4238–E4247. |
| v1 | transcription factor regulation | 1 | 10.1093/molbev/msv058 | Jin, J., He, K., Tang, X., Li, Z., Lv, L., Zhao, Y., … Gao, G. (2015). An arabidopsis transcriptional regulatory map reveals distinct functional and evolutionary features of novel transcription factors. Molecular Biology and Evolution, 32(7), 1767–1773. |
| v1 | binding | 1, 2 | 10.1093/nar/gkac1000 | Szklarczyk, D., Kirsch, R., Koutrouli, M., Nastou, K., Mehryary, F., Hachilif, R., … von Mering, C. (2023). The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Research, 51(D1), D638–D646. |
| v1 | small RNA interactions | 3 | 10.1093/nar/gkp818 | Zhang, Z., Yu, J., Li, D., Zhang, Z., Liu, F., Zhou, X., … Su, Z. (2009). PMRD: Plant microRNA database. Nucleic Acids Research, 38(SUPPL.1), 806–813. |
| v2 | binding | 1, 2, 3 | 10.1093/nar/gku1053 | Lee, T., Yang, S., Kim, E., Ko, Y., Hwang, S., Shin, J., … Lee, I. (2015). AraNet v2: An improved database of co-functional gene networks for the study of Arabidopsis thaliana and 27 other nonmodel plant species. Nucleic Acids Research, 43(D1), D996–D1002. |
| v1 | small RNA interactions | 3 | 10.1093/nar/gku1162 | Yi, X., Zhang, Z., Ling, Y., Xu, W., & Su, Z. (2015). PNRD: A plant non-coding RNA database. Nucleic Acids Research, 43(D1), D982–D989. |
| v2 | transcription factor regulation | 1 | 10.1093/nar/gky1023 | Tong, Z., Cui, Q., Wang, J., & Zhou, Y. (2019). TransmiR v2.0: An updated transcription factor-microRNA regulation database. Nucleic Acids Research, 47(D1), D253–D258. |
| v1 | small RNA interactions | 1, 2 | 10.1093/nar/gkz896 | Huang, H. Y., Lin, Y. C. D., Li, J., Huang, K. Y., Shrestha, S., Hong, H. C., … Huang, H. Da. (2020). MiRTarBase 2020: Updates to the experimentally validated microRNA-target interaction database. Nucleic Acids Research, 48(D1), D148–D154. |
| v1 | transcription factor regulation | 1, 2 | 10.1104/pp.105.072280 | Palaniswamy, S. K., James, S., Sun, H., Lamb, R. S., Davuluri, R. V., & Grotewold, E. (2006). AGRIS and AtRegNet. A platform to link cis-regulatory elements and transcription factors into regulatory networks. Plant Physiology, 140(3), 818–829. |
| v2 | binding | 1, 2, 3, 4 | 10.1104/pp.18.01216 | Dong, S., Lau, V., Song, R., Ierullo, M., Esteban, E., Wu, Y., … Provart, N. J. (2019). Proteome-wide, structure-based prediction of protein-protein interactions/new molecular interactions viewer. Plant Physiology, 179(4), 1893–1907. |
| v1 | binding | 1, 2 | 10.1126/science.1203659 | Mukhtar, M. S., Carvunis, A. R., Dreze, M., Epple, P., Steinbrenner, J., Moore, J., … Payne, T. (2011). Independently evolved virulence effectors converge onto hubs in a plant immune system network. Science, 333(6042), 596–601. |
| v1 | binding | 2 | 10.1126/science.1203877 | Arabidopsis Interactome Mapping Consortium. (2011). Evidence for Network Evolution in an Arabidopsis Interactome Map. Science, 333(6042), 601–607. |
| v1 | binding | 2 | 10.1126/science.1251358 | Jones, A. M., Xuan, Y., Xu, M., Wang, R. S., Ho, C. H., Lalonde, S., … Frommer, W. B. (2014). Border control - A membrane-linked interactome of Arabidopsis. Science, 344(6185), 711–716. |
| v1 | binding | 1, 3 | 10.1186/1471-2105-10-454 | Brandão, M. M., Dantas, L. L., & Silva-Filho, M. C. (2009). AtPIN: Arabidopsis thaliana protein interaction network. BMC Bioinformatics, 10, 1–7. |
| v1 | binding | 3, 4 | 10.1186/1471-2164-10-288 | De Bodt, S., Proost, S., Vandepoele, K., Rouzé, P., & Van de Peer, Y. (2009). Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression. BMC Genomics, 10, 288. |
| v1 | transcription factor regulation | 3, 4 | 10.1186/1752-0509-4-s2-s2 | Srivastava, G. P., Li, P., Liu, J., & Xu, D. (2010). Identification of transcription factor’s targets using tissue-specific transcriptomic data in Arabidopsis thaliana. BMC Systems Biology, 4(S2). |
| v1 | binding | 1, 3 | 10.3389/fpls.2019.00870 | Zhao, J., Lei, Y., Hong, J., Zheng, C., & Zhang, L. (2019). AraPPINET: An updated interactome for the analysis of hormone signaling crosstalk in Arabidopsis thaliana. Frontiers in Plant Science, 10(July), 1–11. |
| v1 | transcription factor regulation | 2 | 10.7554/eLife.00675 | Chang, K. N., Zhong, S., Weirauch, M. T., Hon, G., Pelizzola, M., Li, H., … Ecker, J. R. (2013). Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. ELife, 2013(2), 1–20. |
| v1 | transcription factor regulation | 2 | 10.7554/eLife.07295 | Liu, S., Kracher, B., Ziegler, J., Birkenbihl, R. P., & Somssich, I. E. (2015). Negative regulation of ABA Signaling By WRKY33 is critical for Arabidopsis immunity towards Botrytis cinerea 2100. ELife, 4(JUNE2015), 1–27. |
| v2 | assorted | 0 | n/a | n/a |
CKN ranks
The ranks of CKN edges are as follows:| Rank | Description |
|---|---|
| 0 | manually curated interactions from PSS |
| 1 | literature curated interactions detected using multiple complementary (mostly targeted) experimental methods (e.g. luciferase reporter assay, co-immunoprecipitation, enzymatic assays) |
| 2 | interactions detected solely using high-throughput technologies (e.g. high-throughput yeast two-hybrid, chromatin immunoprecipitation sequencing, degradome sequencing) |
| 3 | interactions extracted from literature (co-citation, excluding text mining) or predicted in silico and additionally validated with data |
| 4 | interactions predicted using purely in silico binding prediction algorithms |
CKN explore options
CKN Explorer
Available at: CKN Explorer
The biomine-like exploration interface allows for interactive search queries of CKN, shortest path, and neighbourhood extraction.
Users can search the available nodes using the search box, and add them to the query, before selecting search. If a single node is in the selection, the search will return the first neighbours, while if multiple nodes are present, the search will return the merge of all shortest paths between the selected nodes. Note that the result is limited to display the top 25 nodes, ranked topologically (page rank).
An option to limit search results to only include certain edge reliability ranks (filtering edges) or genes differentially expressed in particular tissues (filter nodes) is also provided in the left panel.
Right clicking on a node in the result brings up a sub-menu, including expanding node neighbours. Right clicking on the canvas brings up the option to freeze all node positions.
When applicable, the sub-menu of the node also contains a link to query the Arabidopsis identifiers associated with the node in KnetMiner.
Using the "Export" menu, the results of a search can be saved as a edge table, node table, or PNG.