Please note: Plot (Categorical Bar chart) comparing the candidate genes with the other maize genes is generated using a randomly downsampled set of other maize genes. The size of the randomly downsampled genes is equal to the size of the user defined candidate genes.

Example Candidate gene list:

To demonstrate the potential use case of the user candidate gene analysis, we gathered a set of fifty stress genes that were differentially expressed between the control and salt stress samples and used them to identify unique characteristics common among salt stress genes .

Please go through the below explanation for details on table and plot interpretations

Table column interpretation:

The co-expression set of features consist of 12 binary variables defining membership in each of the 12 co-expression models defined by (Hoopes et al., 2019)and are displayed in the table as:


1. WGCNA Module1

2. WGCNA Module2

3. WGCNA Module3

4. WGCNA Module4

5. WGCNA Module5

6. WGCNA Module6

7. WGCNA Module7

8. WGCNA Module8

9. WGCNA Module9

10. WGCNA Module10

11. WGCNA Module11

12. WGCNA Module12


13. Labels

The labels are the classes or the groups the genes are mapped into.The labels can act as both target variable or feature as per the need of the user for solving their specific problem

13.1 No Label

This selection is provided to enable users to view the properties of all genes without labeling them into different gene categories or annotations. This is to let users examine the features of multiple genes and identify common patterns among them. As it involves the inspection of all the genes therefore they work only for "Submit for analysis" button .

13.2 Classical Genes

Classical genes can be defined as the most well-studied genes mainly for their visible mutant phenotype (for example: liguleless3).

13.3 Pan-genome Genes

A gene in a given taxonomic group is either present in every individual (core), or absent in at least a single individual (dispensable).

13.4 Origin Genes

Gene duplication is an important evolutionary mechanism allowing new genetic material and thus opportunities to acquire new gene functions for an organism. There are different origins of duplications such as whole-genome duplications, tandems, etc.


Graph interpretations:

To the top right corner of the plots/graphs, there are options to download plot, zoom-out/zoom in, reset axes, autoscale, toggle spike lines, show closest data on hover, compare data on hover, box select, pan and lasso. Users can also select specific legends to view data only for the selected legends. Details on the interactive plot options are available here:
Interactive graph features

1. Categorical marginal Plot

The Categorical marginal Plots are bar plots showing the frequency distribution of the different categories of the selected gene features alonghwith higlighting the candidate genes. This plot will enable the user to easily identify where thier candidate gene lie among the other maize genes for the selected feature.

2. Categorical Bar chart

The Categorical Bar chart shows the frequency distribution of the different categories in the selected correlation features such as WGCNA Module1. The X-axis in the Categorical bar chart represents the different categories in the selected correlation feature. The Y-axis represents the frequency of the categories in the selected correlation feature. In addition to the graph,to increase the interpretability of the data, We have also included P-values, mean and standard deviations of the selected datasets.

For further details on these features please go through the below paper :
https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.14184