Stress Knowledge Map

Supported by the ADAPT project

SKM logo

Welcome to Stress Knowledge Map!

This is a compilation of knowledge on mechanisms underlying responses of plants to stress, the so called stress signalling network. Of course, responses to stress are tightly connected to growth and developmental signalling, so in some parts these processes are also included to provide a complete picture.

Knowledge was compiled by manual inspection of manuscripts, knowledge provided in several knowledge databases and from datasets published as supplemental materials. Only information on direct physical interaction is included:

  1. Protein - protein interactions
  2. Protein - DNA interactions, e.g. transcriptional regulation
  3. smallRNA - transcript interactions
  4. Enzymatic transformations of metabolites

The signalling network is composed of nodes and connections. Connections are of different types, in line with above listed physical interaction types. Nodes represent different molecular entities:

  1. genes/transcripts/proteins/active proteins
  2. smallRNAs
  3. metabolites

Stress Knowledge Map is currently focusing on the following species: Arabidopsis thaliana, potato, tomato, and poplar, thus only experiments performed on those species are included.

Two compiled networks are available in Stress Knowledge Map:

1 Mechanistic Plant Stress Signalling model (PSS)

(Formerly the Plant Immune signalling model.) In this network only highly reliable interactions are entered, i.e. interactions published in at least one manuscript. This normally means that the results are confirmed by at least two independent approaches. The formalism of knowledge compilation in the database allows for different types of mechanistic modelling, from boolean to ODE and more. For more detailed information on the formalism used see the documentation.

PSS overview
2 Comprehensive Knowledge Network (CKN)

Includes information that is slightly less reliable, that is information from high throughput experiments, e.g. ChIp-Seq and DAP-Seq, large scale PPI experiments, and information from different knowledge-bases, e.g. KEGG for metabolic reactions or STRING. Some predicted interactions are also included, but never interactions inferred from co-expression analysis or similar. The formalism of this database is only network based, thus not compatible with all types of modelling.

To use SKM

You can explore the Mechanistic Plant Signalling model (Explore PSS) or the Comprehensive knowledge network (Explore CKN).

Or download the datasets to perform any type of analysis or modelling yourself: Downloads.

Enter a interaction that is still missing in mechanistic Plant Stress Signalling model: Contribute (note that contributions require an account).

If you have used Stress Knowledge Map in your research please cite:
Carissa Bleker, Živa Ramšak, Andras Bittner, Vid Podpečan, Maja Zagorščak, Bernhard Wurzinger, Špela Baebler, Marko Petek, Maja Križnik, Annelotte van Dieren, Juliane Gruber, Leila Afjehi-Sadat, Wolfram Weckwert, Anže Županič, Markus Teige, Ute C. Vothknecht, Kristina Gruden. (2024). Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses. Plant Communications. doi:10.1016/j.xplc.2024.100920 .

Latest Updates

Training Workshop for Stress Knowledge Map

by Carissa on 2024-06-18

Thank you to all that attended our workshop! The slides are available here: Slides We ... Read more

Celebrating the publication of Stress Knowledge Map in Plant Communications

by Carissa on 2024-06-14

We are thrilled to announce the publication of our article in Plant Communications titled "Stress Knowledge Map: A Knowledge Graph Resource for Systems Biology Analysis of Plant Stress Responses." This comprehensive resource, developed by an international team of experts led by dr. Kristin ... Read more

Please note that NEWT is a client-side application, and therefore relies on your local computer capabilities. Given the relatively large size of PSS, rendering the network may take a while.