Manual page for web server CisCross-FindTFnet

General description

Web server CisCross-FindTFnet is an application for reconstruction of transcription factor regulatory networks (TFRNs) of the input up-regulated (uDEGs) and down-regulated (dDEGs) differentially expressed gene lists.

Input data

CisCross-FindTFnet takes two lists of genes: uDEGs and dDEGs. CisCross- FindTFnet algorithm suppose that input lists are exactly uDEGs and dDEGs. Publicly available gene expression databases, for example the EBI Expression Atlas (Moreno et al., 2022, https://www.ebi.ac.uk/gxa/home) is a good source of qualitative transcriptomic data. The Buttons Load genes allow fill the fields List of DOWN regulated Genes and List of UP regulated Genes or insert gene lists from the clipboard. Genes should be name with TAIR ID, for example AT1G05680. On the web page, there is the recommendation for creating a file (format of genes).

• Length of promoter (bp) – whole-genome annotation of gene promoters as the regions of 500, 1000, 1500, 2000 or 2500 bp upstream to the transcription start sites
• DAP-Seq collection – the available versions for the DAP-Seq peak set collection are (1) Plant Cistrome (O'Malley et al., 2016); (2) CisCross-GEM (GEM-processed); (3) CisCross-MACS2 (MACS2-processed)
• Background – can choose between Araport11 and TAIR10 annotations of the reference genome

  

• Options for the multiple testing procedure are: Benjamini–Hochberg, Bonferroni methods or none. Also it is available to choose the threshold for the lists of enriched TFs taking in further analysis.

  

All required sections contain default values. To run the algorithm of finding targets of TF list among the input gene list push the button Submit.

To test the workflow use the button Example

Output data

The first and the second blocks represent the lists of potential upstream regulators of uDEGs and dDEGs respectively in ascending order of the significance p-value with adjusted p-value (or FDR)

The third block contains the list of all taken in analysis potential upstream regulators with its recognizing type of TF regulation For more information about type of TF regulation please use Omelyanchuk, N. A., Lavrekha, V. V., Bogomolov, A. G., Dolgikh, V. A., Sidorenko, A. D., & Zemlyanskaya, E. V. (2024). Computational Reconstruction of the Transcription Factor Regulatory Network Induced by Auxin in Arabidopsis thaliana L. Plants, 13(14), p. 1905.

The fourth block contains the list of connected TF regulators with the respect to DNA amplification.

The fifth block represents summary information about TF families, which TF were enriched in analysis.

The sixth block is the graphical representation of the fourth block of the output data.

Extending information about TF families assignment

To save results use the button Save below Results section.