Wheat-RegNet: An encyclopedia of common wheat hierarchical regulatory network. Wheat-RegNet catalogues and annotates 224,829 REs in Chinese Spring wheat genome and 79,501 target genes. Meanwhile, Wheat-RegNet depicts a genome-wide map of 189 transcription factors binding sites and constructs the co-expression network by using target genes of transcription factors and differentially expressed genes from public expression data. User can access the regulatory information of any input region or gene via four functions: Regulatory Elements, Transcription Factors, Functional Module and Jbrowse.

Wheat-RegNet provides three search strategies: regulatory elements, transcription factors and Functional module. All search results are presented in an interactive table and image and can be downloaded. Jbrowse visualization function is provided.For regulatory elements search function, Wheat-RegNet provides REs which associate with the gene, and RE's position at the chromosome、histone modification、RE type(active、repress、poised)、Hi-C contaction, correlaction, P_value, regulatory score, pi and motif information. Wheat-RegNet can also provide the specific distribution of these REs in different tissues. For transcription factors search function, this function can search which TFs regulate a certain gene. Users need to enter the Chinese spring wheat gene ID (IWGSCv1.0). The results of TF-to-TF associations and TF-to-Gene associations will be visualized in the form of a network.For functional module search function, users can search one interested gene or a list of genes in which functional module.

This function can retrieve which regulatory elements regulate input genes. When using this function, users need to enter the Chinese spring wheat gene ID (IWGSCv1.0) or genomic regions.Additionally, Wheat-RegNet integrates orthologous genes from 22 whole-genome sequenced species.Users can input gene ID or gene name of these species to search the regulation of orthologous genes in wheat.The following is an example of gene list search.

3.1 Gene List Query

Input one IWGSC RefSeq v1.0 gene id (eg:TraesCS1A01G003000) and click the Submit button to submit the task.

3.1 Result Interpretation

Regulatory element search result.

The header of almost every column in the table has detailed information about the header, you just need to put the mouse on the icon.We will introduce the meaning of these headers in the table in detail here.

1. Checkbox:You can select the regulatory element you are interested in through the check box, and then click the Heatmap of Select REs button to view its expression in different tissues and different processing conditions
2. RE_ID:This is the code we named each regulatory element. The first CS stands for Chinese Spring, and RE stands for the regulatory element. The next is the chromosome where the regulatory element is located. The final number is defined based on the total number of regulatory elements, which is from 0000001 to 0842025
3. Chr:This represents the chromosome where the regulatory elements are located.
4. Start:This represents the starting position of the chromosome where the regulatory element is located.
5. End:This represents the end position of the chromosome where the regulatory element is located.
6. Histone_Mod:The combination of histone modifications on regulatory elements.
7. Type:We predicted the function of the regulatory elements based on the combination types of histone modifications on the regulatory elements, which are active、repress、poised and others.Acitive means to increase gene expression, repress means to suppress gene expression, poised means temporarily no effect, others means that its effect on target genes is not yet known
8. Hi-C_Con1: Hi-C contaction1 were measured based on the normalized read pair density bridging the constituent regions using published data PRJEB25248 which retrieved from the BioProject database.
9. Hi-C_Con2: Hi-C contaction2 were measured based on the normalized read pair density bridging the constituent regions using published data GSE133885 which retrieved from the Gene Expression Omnibus database.
10. Cor:Correlation represents for peason correlation coefficient of the epigenetic activities(a 84-element vector, i.e., density of three epigenetic marks under 14 conditions with 2 replicates) between the promoter peak and distal peak.
11. R_Score:Regulatory Score to measure the confidence of regulatory relationship between RE and gene.

You can click RE ID to view the relationship between regulatory elements and genes in Jbrowse.

This function can retrieve which transcription factors regulate input genes. Users need to enter the Chinese spring wheat gene ID (IWGSCv1.0). The results of TF-to-TF associations and TF-to-Gene associations will be visualized in the form of a network. For each node, it can be clicked to view the function annotation information

1.Gene List Query.

2.Transcription factor search result.

3. Functional annotation information for each node.

This function can retrieve the module where the input gene(s) is/are preferentially located, the function of the module, as well as the TFs regulating the module.

1.Gene List Query.

1.Functional module search result.

You can choose to enter the gene ID or enter the genomic regions.

In the selection panel, the detailed information for each sample is provided and could be selected for visualization.

Track your job is using job id, which will be generated as the task submitted. You can enter your job id in the search box to check the status of the job. If the job is completed, the result page will show up. Currently, the job result will be kept in our server for at least two weeks.

9.1 Epigenomic data Cite :

Wang, M., Li, Z., Zhang, Y., Zhang, Y., Xie, Y., Ye, L., Zhuang, Y., Lin, K., Zhao, F., Guo, J., et al. (2021). An atlas of wheat epigenetic regulatory elements reveals subgenome divergence in the regulation of development and stress responses. Plant Cell 33:865-881.

Tracks for all sequencing data can be visualized through our local genome browser (http://bioinfo.sibs.ac.cn/dap-seq_CS_jbrowse/)

9.2 DAP-Sequence data Cite :

The DAP-sequencing data have been submitted to the NCBI Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) under accession number GSE192815

9.3 GWAS data Cite:

Blake, V. C., Birkett, C., Matthews, D. E., Hane, D. L., Bradbury, P., & Jannink, J. L. (2016). The Triticeae Toolbox: Combining Phenotype and Genotype Data to Advance Small-Grains Breeding. The plant genome, 9(2). Data Website (https://wheat.triticeaetoolbox.org)